Their best top-tier league finish was fourth in the 2003–04 and 2008–09 seasons, with Brazilian striker Nenê winning the Bola da Prata for top scorer with 20 goals in the latter.

They have played in the UEFA Europa League on five occasions between 2004 and 2014, beating Zenit St. Petersburg in the play-off round and taking third place in the group stage in 2009–10.

[5] Stars of this team included Brazilians Paulo Assunção (defensive midfielder) and forward Adriano (16 and 19 goals in respective seasons), both of whom later played for FC Porto.

[6] Nacional's debut European season in the 2004–05 UEFA Cup ended in the first round with a 4–1 aggregate loss to Spain's Sevilla FC.

[8] Manuel Machado led the team to fifth in 2005–06, again reaching the UEFA Cup, but left due to his wife and children living in continental Portugal.

Brazilian forward Nenê earned the Bola da Prata for top scorer with 20 goals, three more than Benfica's Óscar Cardozo and Sporting CP's Liédson.

Nacional started the 2009–10 season without Nenê, who was sold in June to Cagliari Calcio of the Italian Serie A for a fee potentially rising to €10 million.

[13] Nacional were eliminated in the group stage, third behind SV Werder Bremen and Athletic Bilbao but ahead of FK Austria Wien.

[14] In 2010–11, former club players Predrag Jokanović and Ivo Vieira led the team to 6th and a European return, as well as the semi-finals of the Taça da Liga for the first time (at Porto's expense), losing 4–3 to Paços de Ferreira.

In the following season, following Europa League playoff elimination by Birmingham City, the team made the national cup semi-finals again, losing 5–3 on aggregate to Sporting.

[15] In his fourth of five spells as Nacional manager, Machado led the team to 5th in 2013–14, making the Europa League playoffs and falling at the first hurdle 5–2 on aggregate to FC Dinamo Minsk of Belarus.

[17] The 2016–17 season, which included Jokanović's fourth spell as manager, ended with relegation in last place, a conclusion to 15 years in the top flight.