The Bundesliga club said Gramlich, who had been club boss in the late 1930s and then again from 1955-70, had been an active member of the Nazis, becoming a party member as well as a member of the SS.
"Rudolf Gramlich approvingly accepted the violent reign of National Socialism," Eintracht president Peter Fischer said at the club's annual meeting on Sunday.
"This is documented through his leadership of the club that conformed with the regime, his membership of the SS and the NSDAP, two criminal organizations, and especially through his participation in the German terror regime in the occupied territories."
Frankfurt had used the Holocaust research institute Fritz Bauer to look into the lives of former club presidents during the Nazi years.
Gramlich, who died in 1988, had been president when Frankfurt won their only German league title in 1959 and reached the European Cup final in 1960.
"We are convinced that the facts, that played at the time of his being named honorary president... must today be evaluated differently," Fischer said."An honorary president, no matter how positive his contribution to the club, must also be morally and ethically a role model for the youth, the membership and society."