Aytekin refereed his first Bundesliga match on 27 September 2008 when Hertha BSC played FC Energie Cottbus in Berlin.

Notably, Aytekin was the referee of the 2016–17 UEFA Champions League round of 16 second leg match between Paris Saint-Germain F.C.

The final score of the match was a famous 6–1 victory for Barcelona,[3] while the Catalan club had lost by 4 goals to 0 in the first leg.

[4] After the match, PSG lodged a complaint[5] for ten refereeing errors with UEFA, which, without suspending him, de facto dismissed Deniz Aytekin from the major European posters,[6][7] entrusting him with only a few minor group matches in the UEFA Champions League the following two seasons.

[9] On 28 July 2022, Aytekin announced that he had put an end to his international career, and that he would only continue refereeing at a national level in Germany.