The 26-year-old, whose Freiburg contract was due to expire at the end of the season, will join his new club in the summer.
Frankfurt manager Armin Veh told reporters at a press conference: "He is an exceptional midfielder. You just have to congratulate Eintracht Frankfurt on signing Jan Rosenthal.
"I have been tracking his career for several years and wanted to capture him before when I was manager of VfB Stuttgart. Back then it did not work out.
"Jan Rosenthal is a clever player. He can feature as a striker and in attacking midfield. He could even play on the outside of midfield or in a holding position in the centre. He is a versatile player."
Frankfurt currently sit fifth in the Bundesliga table.