Reja managed Vicenza, Napoli, Lazio and Atalanta in Serie A. Reja began his career with the SPAL youth squad, coached by Paolo Mazza, playing in midfield alongside lifelong friend Fabio Capello, and other notable players such as Louis Pasetti and Adriano Zanier.

In 1965, Reja joined Capello in Serie A, in the SPAL first team, earning an appearance with the Italian U-23 squad.

Next year he remained at Vicenza and led his team back to Serie A, but promptly relegated one more time in 2001.

[7] He turned the fortunes of a club in dismay, guiding it out of the relegation zone and into a mid-table finish in the season.

The 2010–11 season for Lazio started in an astonishing way, with the team surprisingly heading Serie A with a four-point advantage to runners-up Inter after nine games, thanks to Reja's abilities in relaunching players such as Mauro Zárate, Cristian Ledesma and Stefano Mauri, as well as introducing new key signings such as Brazilian international Hernanes.

[8] After the sacking of Vladimir Petković, Reja returned to Lazio for a second spell on 4 January 2014, completing the season in ninth place.

[9] Reja was appointed trainer of Atalanta on 4 March 2015 with the team three points above the relegation zone after the dismissal of Stefano Colantuono.

[11] On 17 April 2019, Albania signed Reja to a seven-month contract after fellow Italian Christian Panucci was dismissed the previous month.

[12][13] On 2 March 2023, just a few months after the end of his contract with the Albania national team, Reja returned into management as the new head coach of Slovenian PrvaLiga bottom-placed club ND Gorica.