The Austrian endured a torrid time at Oakwell, winning just once in 15 Championship games in charge after taking over in the summer following the departure of Valerien Ismael to West Brom.
The 47-year-old has presided over a desperate seven-match losing sequence, with the latest arriving in a 2-1 reverse at Bristol City on Saturday.
It extended the Reds’ run without a win to 13 matches.
Barnsley will now begin the search for Schopp’s permanent successor as they look for a sixth permanent head coach in three and a half years.
The Oakwell outfit are fourth points adrift of safety ahead of Wednesday night’s vital relegation six-pointer against Derby County. Barnsley welcome Hull City in another crunch survival encounter on Saturday.
Barnsley CEO Khaled El-Ahmad said: “On behalf of everyone at Oakwell, I would like to thank Markus for the last few months and wish him well for the next step in his career.
“I would like supporters to know that the process for finding a suitable replacement is underway and we will announce a new appointment in due course.”
Markus Schopp added: “I would like to thank all those who have accompanied me in this short but very intense time. It is a pity that our hard work was not reflected in the results. I wish the club all the best for the future and that they will achieve all their goals.”
Joseph Laumann will take charge of first team affairs on a temporary basis, starting with