Kiyonari's introduction to motorsport came through motocross in 1988, a discipline he later admitted he did not particularly enjoy. He transitioned to circuit racing in 1996 and entered the All-Japan 125cc Championship in 1998, competing in that class through 1999. The 2000 and 2001 seasons were spent in the All-Japan 250cc Championship, where results were modest — his best finish in the period was ninth at the 2000 Suzuka 8 Hours.
The breakthrough came in 2002 when Kiyonari switched to the All-Japan ST600 Championship and dominated it, winning four races to claim the title. He also claimed a victory in the All-Japan Superbike Championship at TI Aida that year.
From 2002 into 2003, Kiyonari served as official test rider for Honda Racing Corporation. Following the death of Daijiro Kato at the 2003 Japanese Grand Prix, Gresini Racing required a replacement and team principal Fausto Gresini contacted Kiyonari to join from the French Grand Prix for the remainder of that season. He collected eight minor points finishes in the 500cc-class successor series, placing 20th overall with a best result of 11th.
After finishing sixth in the 2004 British Superbike Championship in his debut full season, Kiyonari announced himself dramatically in 2005 by winning the opening four rounds. A heavy crash in round five left him with an ankle injury, and while he returned in round nine and retook the championship lead from teammate Michael Rutter, the improving Ducati of Gregorio Lavilla eventually overhauled him and he settled for runner-up.
In 2006, Kiyonari delivered a defining performance at the penultimate Silverstone round, recording a double victory to keep his title hopes alive. In the double-points finale at Brands Hatch, a race-one win under safety-car conditions gave him breathing room. Needing only a third-place finish in the final race, he crossed second behind Leon Haslam and claimed his first BSB title by eight points.
The 2007 defence began uncertainly, with Jonathan Rea and Leon Camier initially showing strong form on their Hondas. Kiyonari found his rhythm with a double win in round three and a further victory at Oulton Park. He wrapped up his second consecutive championship at Brands Hatch.
After spending 2008 and 2009 in the Superbike World Championship, Kiyonari returned to BSB in 2010 with HM Plant Honda alongside Josh Brookes. A double win at Mallory Park was among the highlights, and he secured his third BSB title that season — his most spread-out of the three, coming after a three-year absence from the domestic series.
He remained with HM Plant Honda in 2011 and finished sixth overall. In 2013 he returned to BSB with Samsung Honda, again finishing sixth. A move to Buildbase BMW in 2014 marked the first time in his career he raced machinery other than Honda, achieving second place in that year's championship standings. He later rode for Suzuki in 2016 before returning to Japan for the 2017 and 2018 All-Japan JSB1000 Championship.
Kiyonari joined Ten Kate Honda for the 2008 Superbike World Championship, partnering Carlos Checa and Kenan Sofuoglu. He came agonisingly close to a first SBK win at Monza's race two, running at the front going into the Parabolica before going wide on the exit; Noriyuki Haga edged him by 0.051 seconds. His first two World Superbike victories came at Brands Hatch, beating Troy Bayliss in race one and Noriyuki Haga in race two. He added a further wet-weather win at Donington Park, visibly sliding the rear of his Honda on numerous occasions. A collarbone fracture sustained in testing at Magny-Cours caused him to miss the French round. He finished ninth overall in 2008, and remained with Ten Kate Honda for 2009 — now alongside Carlos Checa and Jonathan Rea — to finish eleventh.
The Suzuka 8 Hours endurance race became a defining venue for Kiyonari. He won in 2005, 2008, 2010, and 2012, making him among the most decorated riders in the history of the event. His 2008 victory came alongside former Ten Kate teammate Carlos Checa. The 2012 win came representing Honda in the Asia Road Racing Championship context.
For 2012, Kiyonari led the Boon Siew Honda Malaysia Racing team in the FIM Asia Road Racing Championship, targeting the SuperSports 600cc title. He won the 2012 Asia Road Racing Championship, adding continental honours to his domestic and endurance achievements.
Kiyonari's three British Superbike titles — spread across 2006, 2007, and 2010 — made him one of the series' most successful riders of the 2000s and the standout example of a Japanese rider achieving sustained success in what is historically a domestic-talent-dominated championship. His combination of smooth riding style, mechanical empathy with Honda machinery, and ability to perform under championship pressure earned him a devoted following among British motorsport fans. He retired from professional racing after the 2018 Japanese domestic season.