McIntyre’s assistant Jimmy Boyle has also left the club with immediate effect.
McIntyre was appointed in October 2018, succeeding Neil McCann, and recorded four wins, seven draws and 20 defeats in his 31 matches in charge - although Dundee’s statement recorded just three wins for the former Ross County boss.
The Dark Blues’ relegation from the Ladbrokes Premiership was confirmed earlier this month following a home defeat at the hands of Hamilton Accies.
A statement from the club read: “We would like thank Jim and Jimmy for their efforts while in charge and wish them all the best for the future.”
McIntyre’s first game in charge was a 4-0 defeat to Livingston at Almondvale, followed by a 3-0 home defeat to Hearts. Celtic then scored five without reply at the Kilmac Stadium and Motherwell recorded a 1-0 home win over the Dark Blues as McIntyre lost his first four matches in charge.
In January, Dundee were held to a 1-1 draw at home in the Scottish Cup fourth round by Championship side Queen of the South. The Doonhamers recorded a comprehensive 3-0 victory in the replay at Palmerston.
Under McIntyre, Dundee shipped more than 60 goals and recorded wins over Hearts, Hamilton and Livingston twice.