He was a rather unknown coach in German regional football, when, at the age of 44, he became the assistant manager of Arminia Bielefeld. Arminia began that season with only five points out of ten matches, so that the manager Markus von Ahlen who had brought Krämer to Arminia before had to leave and Stefan Krämer became Arminias interim manager. Because of his surprising success he became Arminias main manager later on. In his first season Arminia still had some weak phases but in the 2012–13 season he managed Arminias qualification for the 2. Bundesliga. He also managed Arminias qualification for the second round of the DFB-Pokal twice, where Arminia each time had an exciting match against Bayer Leverkusen. Thus, he had become very popular in Bielefeld and developed a high identification with the club (including a huge tattoo on his chest). From September 2013 onwards, Arminia played a very weak season, so that Krämer was dismissed in February 2013. He finished with a record of 42 wins, 23 draws, and 27 losses. Also in Cottbus he was complimented for his high commitment but had to leave because the weak beginning of his second season there. He finished with a record of 17 wins, 14 draws, and 18 losses with Energie Cottbus.
He was appointed as the head coach of Rot-Weiß Erfurt on 30 December 2015. On 2 October 2017, he was sacked.