Fitzpatrick entered the British Saloon Car Championship (BSCC) with Team Broadspeed from 1963, driving Austin Mini Cooper S machinery. In 1964 he switched briefly to the Cooper Car Company's factory effort, claiming his first class victory and finishing runner-up to Jim Clark in the championship. Returning to Broadspeed in 1965, he won three podiums before his championship-defining season of 1966. That year Broadspeed was contracted by Ford to run 1000cc Ford Anglias; when co-driver Peter Proctor was injured in a serious accident at Goodwood, Fitzpatrick carried the charge on his own and won the championship outright. He remained a BSCC front-runner through 1971, accumulating further class victories before redirecting his career toward endurance racing.
Fitzpatrick's move into longer-format racing proved transformative. In 1971 he joined Ford Köln for the European Touring Car Championship (ETCC), partnering Jochen Mass at selected endurance events and winning the Austria-Trophäe at the Salzburgring. He simultaneously drove a Porsche 911 S for the Kremer team in the inaugural European GT Championship, winning five of nine races to claim the title by a dominant margin over Claude Haldi, and collecting the prestigious Porsche Cup.
He won the European GT Championship a second time in 1974, again with the Porsche 911 Carrera RSR under the Kremer banner, adding a second Porsche Cup in the process. Throughout the mid-1970s he interspersed ETCC campaigns — with BMW Team Schnitzer, BMW Italia, and Ford Köln — with Group 5 and World Championship for Makes (WCM) outings. In 1976, driving a BMW 3.5 CSL with Tom Walkinshaw, he won the Silverstone 6 Hours after the lead Porsche struck trouble, winning by just twenty metres. The same season he co-drove the Peter Gregg / Brian Redman BMW 3.0 CSL to victory at the 24 Hours of Daytona after his own car retired, and won the Hardie-Ferodo 1000 at Bathurst in a Holden Torana L34 with Bob Morris.
With the Gelo Racing Porsche 935 from 1977 onward, Fitzpatrick developed an outstanding record in Group 5 endurance racing. He won the Mugello 6 Hours twice (1978 and 1979), the Silverstone 6 Hours in 1979, and the ADAC 1000 km Rennen, frequently partnering Bob Wollek and Manfred Schurti.
In 1980 Fitzpatrick joined Dick Barbour Racing in the IMSA Camel GT Championship, piloting the Porsche 935 K3. He swept the title convincingly, winning seven of fourteen races — including the 12 Hours of Sebring and the Los Angeles Times Grand Prix — and secured the Porsche Cup for a third time. His dominance in the 935 K3 established him as the premier sports car pilot in North America that season.
After Dick Barbour encountered financial difficulties, Fitzpatrick founded John Fitzpatrick Racing (JFR) in 1981 with Sachs sponsorship, assisted by the Kremer brothers. The team achieved immediate success, winning at Road Atlanta in its debut season. Through 1981 and 1982 Fitzpatrick continued to score victories in IMSA, adding the Los Angeles Times Grand Prix in both years and winning multiple rounds at Mid-Ohio, Lime Rock, and Road America.
The team's ambition escalated with the acquisition of Porsche 956 prototypes for the 1983 World Endurance Championship. JFR became the first privateer to field a multi-car team of 956s, and Fitzpatrick and Derek Warwick famously defeated the works Porsche team at Brands Hatch in soaking conditions, benefiting from aerodynamic modifications developed in the team's own program. A Porsche 962 was added for 1984 under Skoal Bandit sponsorship, but declining finances eroded competitiveness. Fitzpatrick's last significant result as a driver came at the 1985 Norisring round of the WEC. He retired from driving after the 1000 km di Mugello, sold the team and all its equipment to Jochen Dauer, and relocated to Spain.
Fitzpatrick's career spanned more than two decades at the highest level of touring car and endurance racing, encompassing championships in Britain, Europe, and North America. He remains one of comparatively few drivers to have won major titles in saloon cars, GT racing, and prototype endurance racing — each time as a respected Porsche specialist. His team, JFR, pioneered private Porsche 956 operation at a time when the works cars dominated world endurance racing.