Born in Castelo de Paiva, Aveiro District, Rui Pedro joined Porto's youth system in 2012, aged 14.

On 24 January 2015, at the age of 16, he made his professional debut with their B team, coming on as a late substitute in a 1–0 away loss against Oliveirense in the Segunda Liga.

[3] Four days later, also from the bench, he played his first match in the UEFA Champions League, as the hosts defeated already qualified Leicester City 5–0 to also reach the knockout stage;[4] late in the year, UEFA.com selected him as their "weekly wonderkid".

[10] From January 2021 to June 2022, Rui Pedro continued competing in his country's second division with Penafiel,[11] but he only managed to score five times in all competitions during his tenure.

[14][15] Rui Pedro was deemed surplus to requirements by manager Zoran Zeljković in January 2024 due to contract issues, in spite of leading the team and league in scoring and having been voted Player of the Month for the previous November.