At the start of 1996–97 season, he signed for Grazer AK, making his debut in place of the unfit first-choice keeper, in the autumn 1996 UEFA Cup second-round game against Internazionale at the Stadio Giuseppe Meazza in Milan.

He made twenty-four appearances in his lone season with Grazer AK, before a high-profile transfer to Arsenal in the Premier League, where he was understudy to the experienced David Seaman.

During the 1997–98 season, Seaman was injured and Manninger covered for him, enjoying a spell of six clean sheets in a row in the league, a joint club record.

After the Gunners bought Richard Wright in 2001,[3] Manninger became number three at Arsenal, and spent the 2001–2002 season on loan at Italian side Fiorentina, where he made twenty-four appearances for the Tuscan club.

In July 2005, Red Bull Salzburg re-signed Manninger from his parent club Bologna, and during season 2005–06 he made sixteen appearances.

He started the season as the club's first choice keeper, but he was injured and replaced by Greek international Dimitrios Eleftheropoulos, who retained the first team goalkeeper's jersey once Manninger was fit again.

In July 2008, as a non-contract player, he returned to Austria for another spell with Red Bull Salzburg, but before the season started, he had signed for Udinese, where he replaced the Juventus-bound Antonio Chimenti.

However, in a career of brief moves, he stayed with the north east Italian club for just two weeks, before being signed by Juventus as backup for Gianluigi Buffon and Chimenti in August 2008.

Following an injury to Buffon during the 2010 World Cup, Juventus signed Marco Storari from Milan in the summer of 2010, and Manninger was demoted to the role of the club's third–choice goalkeeper.

[20] In his early career, he was considered to be a good back-up keeper, but was occasionally accused by pundits of lacking the ability to cope with pressure which was necessary for him to succeed in a starting role.