In the early years of the UAAP, the NU Bulldogs were a competitive team in the league, winning a title in 1954. However by the 1980s, NU was perennially in the bottom ranking of the team standings. In the late 1990s, they improved their ranking by moving up to the middle of the team standings with now PBA stars Danny Ildefonso and Lordy Tugade in their team roster, but still failed to make it to the Final Four.
In 2001, the Bulldogs made a surprise trip to the Final Four. They were led by Jeff Napa who tied the record of UE's Allan Caidic for the most number of three-points made in a single UAAP game. However, they were not able to advance to the Finals as they were beaten by the La Salle Green Archers in their Final Four series.
After season 64 (2001-02), the NU Bulldogs returned to their mediocre performance despite having outstanding players such as Rey Mendoza, Edwin Asoro, both members of the Mythical Five in separate seasons and Jonathan Fernandez, who found some success playing for the PBL's Harbour Centre squad and the SEABA RP team.
In the last quarter of year 2008, the family of Henry Sy of SM Shoemart acquired majority (60%) ownership of the National University. Aside from improving school facilities, the new management has included in their corpoarate plan the improvement of NU's sports programs. After ten years, the National U Bulldogs made it again to the UAAP Final Four in 2012.
The Bulldogs have found recent success in the UAAP baseball tournament. After years of falling to the bottom of the team standings, NU has made it four consecutive times to the Final 4, from season 72 (2009-10 ) to season 75 (2012-13). In season 74 (2011-12) they not only made it to the Finals but also won the championship, their third since 1965. Again they repeated their Finals appearance the following year, season 75 (2012-13). This time however, they were not as fortunate. They finished runner-up to Ateneo.
This is the school's ranking in the three most popular sports in UAAP since 1986, the year the UAAP became an 8-team league. NU returned to participate in the men's football tournament in season 75 (2012-13).