Kiyonari began racing in 1988 in motocross before switching to circuit racing in 1996. He competed in All-Japan 125cc racing from 1998 to 1999, moved to the 250cc domestic class from 2000 to 2001, and then claimed the All-Japan ST600 championship in 2002 with four victories.
During 2002 and 2003, the Honda Racing Corporation employed him as an official test rider. Following the death of main rider Daijiro Kato at the 2003 Japanese motorcycle Grand Prix, Fausto Gresini personally called Kiyonari to join Gresini Racing for the remainder of the MotoGP season. He accumulated eight points finishes and ended the year 20th overall, with a best result of 11th.
Kiyonari moved to the British Superbike Championship (BSB) in 2004, finishing sixth. The following year he won the first four races of the season before a heavy ankle injury forced him out at round five. He returned and contested the title before finishing runner-up to Gregorio Lavilla's Ducati.
In 2006, Kiyonari secured the BSB title in dramatic fashion. A double victory at Silverstone in the penultimate round kept him in contention, and in the double-points finale at Brands Hatch, a second place in the final race — behind Leon Haslam — was enough to take the championship by eight points. He defended the title in 2007, overcoming a strong challenge from Gregorio Lavilla to win the championship for the second consecutive year.
After two seasons in the Superbike World Championship with Ten Kate Honda (2008–2009), Kiyonari returned to BSB in 2010. He won races at Cadwell Park and Mallory Park, ultimately claiming his third British Superbike title. Subsequent seasons saw him finish sixth in 2011 and sixth again in 2013, riding for Samsung Honda. He later raced for Buildbase BMW and then Suzuki — his first departures from Honda machinery in his career.
Kiyonari made his World Superbike debut in 2008 with Ten Kate Honda, partnering Carlos Checa. He came close to victory at Monza in only the second round, finishing third by a margin of 0.051 seconds after going wide at the final corner. His first World Superbike victories came at Brands Hatch: race one against Troy Bayliss and race two against Noriyuki Haga. He added a further wet-weather win at Donington Park. He finished ninth in the championship that year. In 2009, riding alongside Checa and Jonathan Rea, he completed the season 11th overall.
Kiyonari demonstrated equal prowess in endurance racing, winning the Suzuka 8 Hours four times: in 2005, 2008, 2010, and 2012. His 2008 victory came alongside former World Superbike teammate Carlos Checa. He held the record of most Suzuka 8 Hours wins among then-active riders.
For the 2012 season Kiyonari led Malaysian team Boon Siew Honda Malaysia Racing in the FIM Asian Championship, winning the 2012 Asia Road Racing Championship in the SuperSports 600cc class.
Kiyonari's triple BSB titles and sustained competitiveness across multiple championships — including Grand Prix, World Superbike, British Superbike, and Asian series — made him one of the most accomplished Japanese riders to emerge in the international superbike arena. His style and personality earned him a devoted following among British motorcycle fans, a connection rare for overseas riders competing in what is typically regarded as a domestic series.