In a statement, the company said Hakan Samuelsson, a 58-year-old Swede who had run the company since 2005, was "convinced that there should be a fresh start at the highest level of the company."
MAN said it had appointed Georg Pachta-Reyhofen as interim replacement.
One of Europe's leading manufacturers of commercial vehicles, engines and mechanical engineering equipment, MAN employs around 49,500 people worldwide, last year posting sales of €15 billion ($22 billion).
The firm has been battered by the global economic crisis, recently announcing that its net profit had collapsed in the third quarter to just €6 million from €302 million a year earlier.
It has also been embroiled in a scandal that has seen the firm suspend two senior managers because of suspicions that it made bribes in order to win contracts.