[citation needed] Sheppard came to the United States in 1961 and in 1966 won his first race with his horse Haffaday in a steeplechase event at My Lady's Manor, Maryland.
At Monmouth Park Racetrack his trainee Arcadius took the $100,000 Helen Haskell Sampson Stake (NSA-G1) by a length under Brian Crowley.
[6] The 5-year-old horse was bred and owned by longtime client George Strawbridge Jr. and his Augustin Stables.
[7] Jonathan remarked to the Times Union, “I said if I didn’t win one (at Saratoga) this year, I wouldn’t come back”.
[9] In 2008, Sheppard joined fellow Hall of Fame inductee Sidney Watters, Jr. as the only men in American racing to have trained a champion over both jumps and on the flat.
As of 2010, Sheppard's horses had won twelve Eclipse Awards:[citation needed] Sheppard died due to complications from late-stage lyme disease at his home in Hollywood, Florida, on August 27, 2023, at the age of 82.