Kuyt spent three years playing at Fenerbahce after leaving Liverpool in 2012 and was hired as an assistant coach to Ismail Kartal in the summer.
Kartal resigned on Tuesday after Fenerbahce lost 2-1 to rivals Galatasaray, a result which leaves them fifth in the Turkish Super Lig.
Fenerbahce next face Goztepe in the league on Saturday before hosting Liverpool in the Champions League on Wednesday, November 4 at 17:45 UK time.
Kuyt was a fan favourite at Liverpool, scoring 71 goals in 285 appearances from 2006 to 2012. He won the League Cup with the club in 2012 and scored in the 2006/07 Champions League final defeat to AC Milan.
After retiring in 2017, he had managerial stints with ADO Den Haag, Beerschot and FC Dordrecht, before returning to Fenerbahce.
Fenerbahce are 31st in the Champions League league phase with two points from three matches, while Liverpool have won all three of their matches.
A statement from the Turkish club said: "Following the resignation of Ismail Kartal, our club has appointed Dirk Kuyt as head coach of our first team until a new head coach is appointed."
Fenerbahce are six points behind league leaders Galatasaray and their squad includes Romelu Lukaku and N'Golo Kante.
Kartal, 65, took charge as Fenerbahce manager for the fourth time in June 2026.
Just two months after being appointed he tried to resign following a 1–1 draw against Roma in the Champions League and said he would "never return". They have also been beaten convincingly away to Aston Villa.
But the club rejected Kartal's resignation and he was convinced to stay - but only for six weeks longer.