Nacional reached the
first division for the first time ever with a three-season spell from 1988. Under manager
José Peseiro, the team returned for
2002–03 after winning promotion in third place. The team finished comfortably in 11th, with results including a 1–0 home win over
S.L. Benfica on 28 September 2002 and a 3–2 win at
C.S. Marítimo in the
Madeira derby the following 2 February. Peseiro's successor
Casemiro Mior took the team to a joint-best 4th place in
2003–04, including another home win over Benfica, shortly after that team had knocked them out of the quarter-finals of the
Taça de Portugal. 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. 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. In January 2005, Mior left for
Club Athletico Paranaense in his homeland.
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. The club's second run in European competition again ended at the first hurdle, 3–1 on aggregate to
CS Rapid București of Romania. managed Nacional in five spells between 2005 and 2021 Under the returning Machado in
2008–09, again edged
S.C. Braga for fourth spot. 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. The side also reached the last-four in the
Portuguese Cup, losing on aggregate 5–4 to
F.C. Paços de Ferreira, with the decider coming at the
Estádio da Madeira in the 90th minute. 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. However, in August the club won a European tie for the first time, defeating 2008 champions
FC Zenit Saint Petersburg 5–4 on aggregate in the playoffs of the renamed UEFA Europa League; the team were heading out on the
away goals rule until a
last-minute goal from youngster
Rúben Micael earned a 1–1 draw in Russia. Nacional were eliminated in the group stage, third behind
SV Werder Bremen and
Athletic Bilbao but ahead of
FK Austria Wien. 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. 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. In the
2014–15 Taça de Portugal they made a third semi-final in seven years, again losing to Sporting. 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. Former Portugal international
Costinha was hired in 2017 and won promotion at the first attempt as champions of the
2017–18 LigaPro;
Cape Verde international striker
Ricardo Gomes was the league's top scorer with 22 goals in 36 games and left the club for
FK Partizan in Serbia at the end of his contract. Costinha left after relegation from the
2018–19 Primeira Liga, in which results included a 10–0 loss to eventual winners Benfica. The
2019–20 LigaPro was abandoned due to the
COVID-19 pandemic in Portugal, resulting in promotion for first-placed Nacional; it was the sixth promotion in the career of 34-year-old manager
Luís Freire. The team were immediately relegated in last place, with Freire sacked in March 2021 and Machado seeing out the season in his fifth spell. The team reached the semi-finals of the
2022–23 Taça de Portugal, losing 7–2 on aggregate to Braga, while the league season went to the final day; a 3–2 home win over
Académico de Viseu F.C. after losing at half time saved the team in 14th place while
B-SAD took the relegation playoff position. After 13 seasons with
Hummel, the team announced its new partnership with
Kappa ahead of the
2025–26 season. == Club presidents ==