In his first Serie A campaign with Napoli, Reja guided them to an Intertoto Cup qualification spot, and was confirmed at the helm of Napoli in the 2008–09 Serie A season. He managed to lead the "Partenopei" to the second qualification round of the UEFA Cup, where they were defeated by S.L. Benfica. Napoli rose up to first place in the Serie A table in the first half of the season. After two points in nine games caused the team to fall into the bottom half, Reja was sacked on 10 March 2009, following a 0–2 home loss to Lazio, and replaced by former Italian team boss Roberto Donadoni.