In a 15-year professional career he spent 14 seasons in the Primeira Liga, mainly in representation of Porto and Sporting CP, playing 292 matches and scoring seven goals in the competition.

In July 1998, Rui Jorge signed with Sporting CP, where he would remain for the following seven years, being first choice during most of his stint and adding two more leagues to his trophy cabinet, with the double being conquered in 2002.

[7] His suspension was lifted in May, with the fault placed on Sporting for not notifying authorities of his medical exemption;[8] at the tournament, he was one of four players – three from defence – dropped by Luiz Felipe Scolari after the opening 2–1 loss to Greece,[9] and did not return for the remainder of the competition, which Portugal lost in the final to the same team.

In May 2009, Rui Jorge was appointed Belenenses' head coach for the final two matches of the season, taking over from Jaime Pacheco after a 0–5 home loss against S.C. Braga,[10] with the team eventually ranking second from bottom (being later reinstated).

[12] He led them to the 2015 European Championships in the Czech Republic after ten wins in as many matches in the qualifying phase,[13] and coached them to the second place in the finals following a penalty shootout defeat against Sweden.