Motoyama began karting at age 13 in 1984, winning the A1 class All-Japan Karting Championship in 1986 and A2 class titles in 1987 and 1989. He graduated to the All-Japan Formula Three Championship in 1990 but achieved only limited success in his early seasons, struggling for sponsorship in 1993 and 1994. In 1995 he signed with Dome Racing and finished second in the championship to Pedro de la Rosa.
He also competed in the Japanese Touring Car Championship from 1995 to 1997. In the 1997 season finale at Fuji, Motoyama was involved in a controversial incident in which he intentionally spun championship rival Osamu Nakako after being hit by him, resulting in a one-race suspension from Formula Nippon and a fine of ¥500,000.
Motoyama made his Formula Nippon debut in 1996 with the Funai Super Aguri team run by Aguri Suzuki. His breakthrough came in 1998 with Team LeMans, when he won three races including back-to-back victories at Miné and Fuji to claim his first championship. He finished second to Tom Coronel in 1999, then moved to Team Impul in 2000.
His second title came in 2001 after a dramatic second half of the season in which he overcame a 22-point deficit to Naoki Hattori, winning three of the final four races. The 2002 campaign saw him win five of ten races yet lose the championship by just two points to Ralph Firman.
In 2003, Motoyama claimed his third championship with Team Impul. The season was marked by personal tragedy: his childhood friend and MotoGP champion Daijiro Kato suffered fatal injuries at Suzuka in April, yet Motoyama raced on through grief, winning four times that year. By claiming his third title, he joined Kazuyoshi Hoshino and Satoru Nakajima as only the third driver to win three or more Japanese top-formula championships, and was the first in the Formula Nippon era to do so.
A fourth championship followed in 2005, again with Team Impul, secured with wins at Sugo, Suzuka, and Motegi. His 27 career Formula Nippon victories, 21 pole positions, and four championships remain the all-time records in the Formula Nippon/Super Formula era from 1996 onwards.
Motoyama debuted in the All-Japan GT Championship in 1996 in the GT300 class before stepping up to GT500 in 1997 with Team Impul alongside Kazuyoshi Hoshino. After switching to the Nismo operation in 1999, he scored his first GT500 victory at the Central Park Miné Circuit and finished third in the championship alongside Érik Comas, who won the title that year.
Paired with German driver Michael Krumm at Nismo from 2002, the duo's consistency in 2003 — scoring in all seven rounds and posting four podiums — delivered the GT500 title without winning a race. The following year, Motoyama was given the new Nissan Fairlady Z33 alongside Richard Lyons and won back-to-back championships, opening his 2004 title defense with a win at TI Circuit and adding another at Autopolis.
The R35 Nissan GT-R era began in 2008, and Motoyama and new co-driver Benoît Tréluyer led a 1-2 in the car's debut race at Suzuka. They won three times that year and took the championship, making Motoyama the first three-time GT500 champion. In 2009, his victory at Sugo was his 12th career GT500 win, surpassing Yuji Tachikawa's all-time record. The partnership with Tréluyer continued through 2011, with three wins that season and a championship runner-up finish.
After moving to MOLA in 2013, Motoyama's last GT500 victory came at Chang International Circuit in Thailand in 2015. His final podium in the series came at Sugo in 2017. He drove his last GT500 race at Twin Ring Motegi on 11 November 2018 and announced his retirement as a GT500 driver in February 2019.
Motoyama competed at the 24 Hours of Le Mans four times. His 1998 debut came with NISMO in one of four factory Nissan R390 GT1 cars, finishing tenth overall. In 1999 he drove the new R391 prototype alongside Érik Comas and Michael Krumm, running as high as fourth before retiring with an electrical issue. His most dramatic Le Mans outing came in 2012 in the experimental Nissan DeltaWing alongside Krumm and Marino Franchitti. After being struck by Kazuki Nakajima's Toyota in the Porsche Curves, Motoyama spent two hours attempting roadside repairs — his Nissan mechanics giving instructions from behind the spectator fencing — before ultimately retiring. His final Le Mans entry was in 2014 in the all-electric Nissan ZEOD RC, which retired after completing the first all-electric lap of the Circuit de la Sarthe.
Following championship success in 2003, Motoyama tested for both the Jordan and Renault Formula One teams. He completed 69 laps for Renault at Jerez and was within two seconds of Fernando Alonso's best time, but was unable to secure a race drive.
After retiring from GT500, Motoyama became an executive advisor to Nissan's factory programme. In March 2018 he became team director of B-Max Racing Team in Super Formula. Under his leadership, Nobuharu Matsushita won the team's first race at Suzuka in 2022.
Motoyama's combination of four Formula Nippon championships and three GT500 titles — a record at the time of his final title — makes him the benchmark of Japanese domestic racing success across the major formula and touring car categories.