Hartstein replaced the late Sid Watkins as F1's chief doctor from the start of the 2005 season and has worked at every race since.
As well as his efforts at the tracks, the American also played a key role in developing new medical safety policies for the governing body through his work as chair of the FIA Institute's Medical Training Working Group.
An FIA spokesperson said on Wednesday that no decision had been taken on who will replace Hartstein, and there was no formal explanation as to why Hartstein's contract was not being extended.
Writing on his Twitter account, Hartstein said that he had relished his time in F1.
"Have just been informed that president of the FIA and president of FIA medical commission have decided not to renew my Formula 1 contract," he wrote.
"Not sure about the "whys" of the decision, but not down to me to know. Brazil will therefore be my 247th and last Formula 1 Grand Prix. It's been a life changing experience and something I'll never forget."
- Sid Watkins