Rui began his journey in the acclaimed youth system of FC Porto, where he progressed through the ranks, featuring prominently in its Under-15, U17, and U19 sides. He was subsequently promoted to Porto's B side.
On 9 July 2019, Pires moved on a free transfer to Ligue 2 side Troyes. He make his debut for the club on 26 July in 2–0 win over Chamois Niort. On 26 October, Pires assisted Lenny Pintor who then went on to scored the winner in the 85th minute in a 1–0 win over Lorient. In December, he suffered anterior cruciate ligament injury ending his season prematurely. He ended up making 13 appearances in his first season.[2]
Pires make his returned on 28 September 2020 coming on as a substitution in a 1–0 win over Clermont Foot. He won the French second-tier Ligue 2 with Troyes in the 2020–21 season where he make 19 appearances.
Paços de Ferreira
On 26 July 2021, Pires returned to Portugal and joined Paços de Ferreira on loan.[3] His loan was made permanent after a successful loan.
On 29 June 2023, it was reported by the Portuguese press that Pires had moved to Singapore to play for Lion City Sailors.[4] He was officially announced as the new signing for the team on 14 July 2023 signing a two-year contract however, as the foreign quota for the league slot is full, Pires will be registered in the club 2023–24 AFC Champions League matches instead.[5] On 26 July 2023, Pires make his debut for the club in a friendly match against Tottenham Hotspurs at the Singapore National Stadium. On 20 September 2023, Pires played his first official game for the club in the 2023–24 AFC Champions League group stage fixture against Thai club Bangkok United in a 2–1 lost.
On 18 July 2024, Pires make his league debut in a 5–0 lost to Tampines Rovers. During the 2024–25 ASEAN Club Championship against Indonesian club Borneo Samarinda, he picked up his second yellow card 35 seconds after receiving the first yellow where he sees red for the first time of his career.
