The current Cyclones franchise started in the 1995 as the Louisville RiverFrogs in Louisville, Kentucky. After three years, the team moved to Miami as the Miami Matadors. After the lone season in Florida, the franchise eventually came into the ownership of a group in Birmingham, Alabama, and the franchise went into inactive status while ownership considered locations for their team. Upon the folding of the IHL, the Cyclones name was sold to this ownership group who moved the franchise to Cincinnati to become the new Cyclones.

The first year back in the ECHL ended the team's streak of 90+ point seasons with the Cyclones finishing just 12 points shy despite a 10-game fewer season length. Former Cyclones player Paul Lawless became head coach, as a mid-season replacement for Ray Edwards.

Before the start of the 2003–04 season former Cyclones player and assistant coach Chris Cichocki left the Arkansas RiverBladesin order to return as the Cyclones head coach. Despite his success with Arkansas, Cichocki led the team to their worst season with 54 points and failed to make the playoffs for the second time in team history.

Shortly after ending the season without a playoff berth, in April 2004, the Cyclones suspended operations.With minor league hockey dormant in Cincinnati for a yearon April 21, 2006, the Cyclones announced that they would participate in the upcoming 2006–07 ECHL season. They returned to play their home games at U.S. Bank Arena, joining their two ECHL, Ohio rivals, the Dayton Bombers and Toledo Storm. They then obtained an affiliation with the Montreal Canadiens of the NHL and the Hamilton Bulldogs of the AHL. The Cyclones won their first game back in the ECHL on October 20 against the Pensacola Ice Pilots at U.S. Bank Arena with a score of 3-1. Head coach Chuck Weber was the runner-up for the ECHL's Coach of the Year award for 2006–07 following the season.

In addition to the Montreal/Hamilton affiliation, the Cyclones added the NHL's Nashville Predators and the AHL's Milwaukee Admirals as affiliates in 2007. The Cyclones' 2007–08 season saw the club break numerous franchise and league records. Through 50 games, the Cyclones were 31 games over .500. Attendance at games had increased nearly 40% over 2006–07 and the club had already surpassed their win total from 2006–07 (37). They achieved this mark in 24 fewer games.On February 22, 2008, the Cyclones tied the ECHL record for a single-season winning streak of 14 consecutive games, defeating the Johnstown Chiefs 5–2 in Cincinnati.On February 23, 2008, David Desharnais recorded two assists, extending his streak of games with at least one assist to 18, breaking the existing ECHL record of 17. In the same game, the Cyclones set a new ECHL record for a single-season winning streak of 15 consecutive wins when the Cyclones defeated the Elmira Jackals in a 5–4 shootout.

The team finished the regular season with 115 points, earning them the Brabham Cup regular season championship. Individually, Chuck Weber was named ECHL coach of the year, earning him the John Brophy trophy. David Desharnais claimed three ECHL awards: Most Valuable Player, Rookie of the Year, and the Leading Scorer award with 29 goals and 77 assists for 106 points. In addition, Chad Starling won the award for the highest plus/minus rating.

The Cyclones entered the playoffs and defeated the Johnstown Chiefs four games to none. The Cyclones moved on to take on the Reading Royals, Cincinnati took the series in seven games to claim their second ever North Division playoff title. The Cyclones then defeated the South Carolina Stingrays, 2–1 in overtime, to claim the American Conference Championship in five games. With their victory, Cincinnati also claimed the E.A. "Bud" Gingher Memorial Trophy.

The Cyclones then defeated the National Conference Champion Las Vegas Wranglers in the Kelly Cup Finals, clinching their first championship in team history in six games. After splitting the first two games in Cincinnati (Cincinnati 4–3 and Las Vegas 1–0), the series shifted to Las Vegas, where Cincinnati won games three and five to take a 3–2 series lead. In front of a record setting crowd, 12,722 fans, at US Bank Arena in Cincinnati on June 5, the Cyclones defeated Las Vegas in game six, 3–1, to take the championship and their 71st win of the season. Goalie Cedrick Desjardins was named the Kelly Cup Playoff MVP.

Cincinnati's 2008–09 season was not as successful as the previous one, but they won 41 games for 87 points, repeating as North Division champions. They won a seven-game series against the Wheeling Nailers, including a double overtime game seven win, and swept the Elmira Jackals to win the North Division playoff title. However, the Cyclones were swept by the South Carolina Stingrays in the American Conference Finals.

The 2009–10 season proved to be more successful with 44 wins and 91 points, the wins total being the most in the American Conference. Despite that, the Cyclones finished second in the North Division to the Kalamazoo Wings and fifth in the conference. This led to a rematch with fourth seeded, and defending champion, South Carolina in the first round, where Cincinnati defeated the Stingrays in five games. Veteran captain Barrett Eghotz scored in overtime for the 3–2 win in game five and was the third straight overtime game in the series. The Cyclones then faced the top seeded Charlotte Checkers, defeating the Checkers in game seven with a 2–1 victory.

Cincinnati drew the Reading Royals in the American Conference Final. The seven-game made ECHL history when, after losing the first two at home, then game three at Reading, Cincinnati posted wins of 6–4, 5–0 and 6–3 to force the team's third winner-take-all game in the 2010 playoffs. In front of 5,340 fans, the Cyclones posted a 1–0 win to become the first team in ECHL history, and the sixth professional hockey team in history, to come back from a 3–0 deficit to win a best of seven series. The only goal of the contest was scored by Barret Ehgoetz 13:48 into the game.

The Cyclones defeated the Idaho Steelheads in the 2010 Kelly Cup Final, four-games-to-one. Cincinnati scored game-winning goals within the last minute in the first two games, a 3–2 win on a goal by Mark Van Guilder with 49.2 seconds remaining on May 14, and a 1–0 win the next night, when Mathieu Aubin netted the only goal in the contest and only with 20.1 seconds remaining in regulation. The series shifted to US Bank Arena and witnessed an Idaho victory within the first minute of the second overtime of game three, as Evan Barlow received a pass at the bottom of the right circle and fired the puck into a largely vacated goal, as Cyclones goalie Robert Mayer had committed to the left side.

In front of yet another ECHL playoff record setting crowd of 13,483 at US Bank Arena in Cincinnati, the Cyclones defeated Idaho in game five, 2–1, to take the championship. With the victory, the Cyclones clinched their second Kelly Cup title in three years. The game was also the Cyclones 24th Kelly Cup playoff game, surpassing the club record of 22 postseason games played by the 2008 championship team and is one more than South Carolina (23) had in its title run in 2009. Rookie Cyclones goaltenders Robert Mayer and Jeremy Smith were named co-winners of the Kelly Cup playoffs MVP. Cincinnati finished with a total record of 59–32–4.

The Cyclones underwent several changes before the 2010–11 season when assistant coach Dean Stork became the head coach of the Greenville Road Warriors in June and head coach Chuck Weber was promoted to the American Hockey League as head coach of the Rochester Americans on July 27. On August 12, Cincinnati named Jarrod Skalde as the new head coach. After undergoing this major coaching overhaul and losing a large portion of their roster, the Cyclones earned a seventh seed in the ECHL playoffs, but lost in the first round to Reading Royals, 3 games-to-1.

In 2011, Cincinnati would finish tenth in the conference, marking only the third time in their 20-season history that they did not make the playoffs.The Cyclones made a complete turnaround the next season, beginning the season unbeaten in regulation for the first nine games. Their 42 wins and 92 points won the North Division regular season championship, their third such accolade in six seasons, and placed them second in the Eastern Conference. The season earned head coach Jarrod Skalde Coach of the Year honors. Cincinnati would go on to win a pair of six-game wins against the Toledo Walleye and Gwinnett Gladiators before losing a five-game conference final to the top seeded Reading Royals, who went on to win the Kelly Cup.

On July 9, 2013, coach Skalde accepted an assistant's position with the AHL's Norfolk Admirals, becoming the second consecutive Cyclones coach to be promoted to a higher level. Before the 2014–15 season, Skalde was appointed as Norfolk's head coach.

Cincinnati came back strong under new head coach Ben Simon in 2013–14, with 41 wins and 91 points for a fifth-place finish in the Eastern Conference. Cincinnati would win three series against the Orlando Solar Bears, Fort Wayne Komets, and Greenville Road Warriors, all in six games, earning their third trip to the Kelly Cup Finals. They faced the Brabham Cup winning Alaska Aces, but would lose the series in six games. Despite the loss in the final, Cincinnati goaltender Rob Madore was named Most Valuable Player of the 2014 Kelly Cup playoffs, becoming the first player from the losing team to win the award in the ECHL's 26-year history, and the fourth Cincinnati goaltender to either win the trophy outright or share the trophy. Madore earned the award after leading the ECHL with all 14 of Cincinnati's playoff wins, 1,493 minutes of play, and a Cincinnati record 756 saves while playing every second of Cincinnati's 24 playoff games.

After the season, coach Simon accepted a role with the Toronto Marlies, the top affiliate of the Toronto Maple Leafs. Simon became the third consecutive Cyclones head coach to accept a role in the AHL. Following Simon's promotion, Matt Macdonald became Cincinnati's head coach. In the 2014–15 season, Cincinnati finished fifth in the North Division of the Eastern Conference with a record of 31–30–2–9. The team would miss the playoffs by only three points.

On February 27, 2016, the Cyclones played in front of their first-ever sellout at US Bank Arena with 16,529 fans were in attendance for Teenage Mutant Ninja Turtles Night. While the game was a 3–2 shootout loss to the Indy Fuel, the Cyclones set the record for the largest crowd for a professional hockey game in the 41-year history of US Bank Arena.

After ten seasons, the Nashville Predators and Milwaukee Admirals ended their affiliation with the Cyclones prior to the 2017–18 season. The Cyclones then found affiliations with the Buffalo Sabres and Rochester Americans. This is the second time Buffalo has affiliated with a Cincinnati hockey team, after the Sabres' affiliation with the Cincinnati Swords in the 1970s.

In August of 2018, the Cyclones named Matt Thomas the team’s new head coach.A native of Maple Ridge, BC, Thomas has extensive head coaching experience in the ECHL, spanning 11 seasons with the Atlantic Boardwalk Bullies, Fresno Falcons, and Stockton Thunder from 2002-2013. Thomas served two seasons as an assistant coach with Atlantic City, including helping the Boardwalk Bullies to a Kelly Cup Championship in 2003, before assuming the role of head coach and Director of Hockey Operations with the team prior to 2004-2005. He compiled a 42-22-8 mark in his lone season as Atlantic City’s bench boss, and also served as the head coach for the 2005 ECHL All-Star Game.

He then moved on to Fresno prior to the 2005-06 campaign, leading the Falcons to a 43-15-14 mark along with a trip to the Western Conference Finals. Over the next two seasons in Fresno, Thomas compiled a 76-41-17 record, with trips to the second round of the Kelly Cup Playoffs on both occasions. He coached the Falcons during the first half of 2008-09, leading the team to an 18-10-2 mark before the team ceased operations midseason. Thomas was not out of work for long however, as he was named head coach of Stockton shortly afterand finished the year with a record of 22-16-3, and a trip to the second round of the Kelly Cup Playoffs.

Thomas went on to coach the Thunder for four more seasons, amassing a mark of 141-111-36, reaching the post season each year, including a trip to the 2013 Kelly Cup Finals where they fell to the Reading Royals, 4 games to 1. He enters the 2018-19 campaign as the ECHL’s sixth-winningest coach with a career record of 342-225-80, just one win back of fifth place all time. He is also the all-time leader in playoff games coached with 97, and ranks third with 49 playoff wins.