The club said Thorup had “signed a settlement agreement after receiving his full dues in line with his contract terms”.
Thorup, 56, was appointed in October on a two-and-a-half-year deal following the exit of Spaniard Jose Riveiro.
He guided Al Ahly to the Egyptian Super Cup title with a 2-0 victory over arch-rivals Zamalek, but results tailed off in the latter stages of the campaign.
Al-Ahly finished third in the league, missing out on a place in next season’s African Champions League and settling for Confederation Cup qualification. They were also eliminated in the quarter-finals of the continent’s premier club competition.