Rebić joined Eintracht Frankfurt on a season-long loan on 11 July 2016, reuniting with former national team manager Niko Kovač. After a short battle with mononucleosis, Rebić made his debut on 17 September against Bayer Leverkusen, coming on as a substitute and assisting Marco Fabián for the winning goal in a 2–1 victory. On 5 February 2017 he scored his first goal for his new team to conclude a 2–0 win over fellow Hesse team SV Darmstadt 98 at the Commerzbank Arena. On 27 May, he equalised in the 2017 DFB-Pokal Final, though Frankfurt lost 2–1 to Borussia Dortmund.