McCall led Motherwell to three successive top-three finishes, a Scottish Cup final appearance and the Champions League qualifiers but has decided to end his reign after almost four years - with the club second from bottom in the table.
The club released a statement which revealed that McCall had told board members of his decision late on Sunday afternoon. Assistant manager Kenny Black will take charge of first-team team affairs in a caretaker role.
The statement read: "Everyone at Motherwell FC would like to sincerely thank Stuart for his contribution to the club, which will go down as one of the most successful managerial tenures in our 128-year history.
"We have been acutely aware of results this season, but everyone at Fir Park was confident in his, and the team's, ability to turn things around.
"However, following a long conversation this afternoon, Stuart felt it better for all concerned if he stepped down with immediate effect and we respect that.
"Assistant manager Kenny Black will take charge of first-team team affairs in a caretaker role to allow the board to start the process of recruiting a new manager, which will begin right away."
McCall turned down a number of approaches from Championship clubs in England during his spell at Fir Park and rejected an offer from Sheffield United in the summer of 2013.
The 50-year-old recently admitted he felt "a bit lost and helpless" after a 3-1 defeat by Dundee on October 18 and narrow defeats to Aberdeen and St Johnstone have triggered the end of his tenure as Well boss.