Reja began his career with the SPAL 1907 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. Together, they helped the team win the 1963–64 Campaniato Nazionale Primavera. In 1965, Reja joined Capello in Serie A, in the SPAL 1907 first team, earning an appearance with the Italian U-23 squad. Reja played for two more teams, U.S. Città di Palermo and Alessandria in a long career that lasted until 1975, playing a total of 124 Serie A matches.
Reja started his coaching career in 1979 serving as boss of Serie D team Molinella. Next year he then coached Monselice of Serie C2. In 1989, he coached his first Serie B team, Pescara, of which he was previously the youth squad boss. He successively gained good successes in the same league with Cosenza, Lecce and Brescia, where he won the championship. In fact, he launched the career of notable footballer Andrea Pirlo at Brescia, where Pirlo was a regular member of the squad. However, Reja opted to give up the opportunity to coach Brescia in Serie A, preferring to accept an offer from Torino, another Serie B team, where he then missed promotion defeated in the promotion playoffs to Perugia after a penalty shootout.
During the 1998–1999 season, he was appointed coach of Serie A club Vicenza, thus making his debut in a top division team, but was unable to save the team from relegation. Next year he remained at Vicenza and led his team back to Serie A, but promptly relegated one more time in 2001. In 2001–2002, he replaced Franco Scoglio at the helm of Genoa (Serie B), but to be fired himself only three months later. On 2002–2003, he was appointed in the mid-season by Catania boss Luciano Gaucci to replace John Toshack. On November 2003, he replaced Gian Piero Ventura at Cagliari and guided the rossoblu to second place in the Serie B and promotion to Serie A, but was not confirmed.
In January 2005, Reja was appointed as the manager of the Partenopei, replacing Gian Piero Ventura. He led Napoli to win Serie C1, obtaining promotion to Serie B in 2006, promptly guiding his team to a second consecutive promotion to Serie A in 2007. Napoli hadn't featured in the top tier of Italian Football since 2001. In his first Serie A campaign with Napoli, Reja guided the Azzurri to an Intertoto Cup qualification spot, additionally garnering memorable wins against Internazionale, Udinese, and A.C. Milan.
Due to his recognizable success the year before, Reja 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, thanks to impressive wins against Fiorentina, Juventus, Palermo, and Lazio; the apparent domestic success greatly increased fans' interest and support for the Neapolitan side, despite the club's failures on a continental level.
However, results quickly deteriorated in the second half of the season, with Napoli losing contact with any of the European Cup spots. Reja was ultimately sacked on 10 March 2009, following a 0–2 home loss to S.S. Lazio on the 27th Serie A Matchday, abruptly closing a five-year spell with the Azzuri. He was replaced by former Italian team boss Roberto Donadoni.
Nevertheless, he is largely credited for the general revitalization of the club, by bringing in and launching the careers of Ezequiel Lavezzi, Marek Hamšík, Walter Gargano, Salvatore Aronica, Christian Maggio, and organizing the return of Paolo Cannavaro, a Napoli veteran, thus building a squad with incredible potential.
After a short successful spell as head coach of Croatian side Hajduk Split from August 2009 to February 2010, Reja opted to quit his job in Split in order to become the new manager of S.S. Lazio. He was unveiled as the new Lazio head coach the following day, replacing Davide Ballardini. 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. On 17 May 2012 he resigned from the job, despite the president's pleas for him to stay on.
After the sacking of Vladimir Petković, Reja returned to Lazio for a second spell on 4 January 2014, completing the season in ninth place. On 12 June 2014, he resigned from his role, with Stefano Pioli appointed as his replacement the same day.
Reja was appointed trainer of Atalanta in early March 2015 with the team experiencing a poor run of form, leaving them on 3 points above the relegation zone. As a result, on 4 March 2015 manager Stefano Colantuono was dismissed with Reja replacing him as manager.
Reja was born in the village of Lucinico (Slovene: Ločnik), now a suburb of Gorizia (Slovene: Gorica), near the border between Italy and Slovenia. His father was a Slovene from the village of Vipolže in Brda, Slovenia, while his mother was Friulian. He is fluent in Italian, Slovene, and Friulan. However, his levels of fluency vary: while he is able to speak the standard form of Italian, he only speaks a regional variety of Slovene, strongly influenced by his native Brda dialect.
He is close friends with current Russian national football team boss Fabio Capello. Reja has been married to his wife Livia since 1969; he met his wife while rooming with Capello in Ferrara, at the time playing for SPAL 1907.
SPAL 1907Campionato Nazionale Primavera (1): 1964–65
U.S. Alessandria Calcio 1912Serie C1 (1): 1973–74
BresciaSerie B (1): 1996–97
VicenzaSerie B (1): 1999–2000
CagliariSerie B (Runners-Up): 2003–04
NapoliSerie C1 (1): 2005–06
Serie B (Runners-Up): 2006–07