Flávio helped his team Al Ahly to participate in the FIFA Club World Championship two successive times in 2005 and 2006.

In the FIFA Club World Championship 2006 opening match against Auckland City FC of New Zealand on 10 December 2006, he scored the first goal, helping Al Ahly to a 2–0 win.

He proved to be instrumental in Al Ahly's formation in the next years, scoring many vital goals in critical moments.

Generally, Flávio kept an extremely low profile and rarely appears in the media or give any press statements.

In his last season with Al Ahly (2008–2009), Flávio managed to score Al Ahly's only goal during the Egyptian Premier League play-off against Ismaily, handing the title to Al Ahly for the fifth time in row and rewarding himself with the second personal title of the Egyptian Premier League Top Goalscorer, for the third time as a foreign player in the Egyptian Premier League history after John Utaka with Ismaily during the 2000–2001 season, then Flávio himself formerly during the 2006–2007 season.