2011 Egyptian club Al Ahly signed the forward from Portuguese side Naval, on 19 July 2011, on a three-year contract worth $1.2 million ($400,000 per season).
Fábio Júnior was signed in order to strengthen the forward line, which consisted of the already formidable duo of Mohamed Nagy "Geddo" and Dominique Da Silva.
However, Junior found games hard to come by often being relegated to the bench (or not even featuring in the match line-up) by then coach Manuel José.
Fábio Júnior would mark his return to continental football by scoring the opening goal of the tie against Ethiopian Coffee, in the Round of 32 in the CAF Champions League.
He later featured in the squad for both legs of the Round of 16 tie with Stade Malien, but was an unused substitute in both matches, with Ahly winning 3-2 on aggregate, to reach the Quarter-finals.