Seasonality of the Mindanao Current (MC)/Undercurrent (MUC) system is investigated using moored acoustic Doppler current profiler (ADCP) measurements off Mindanao (8°N, 127.05°E) and ocean model simulations. The mooring observation during December 2010 to August 2014 revealed that the surface‐layer MC between 50–150 m is dominated by annual‐period variation and tends to be stronger in spring (boreal) and weaker in fall. Prominent semiannual variations were detected below 150 m. The lower MC between 150 and 400 m is stronger in spring and fall and weaker in summer and winter, while the northward MUC below 400 m emerges in summer and winter and disappears in spring and fall. In‐phase and out‐of‐phase current anomalies above and below 150 m were observed alternatively. These variations are faithfully reproduced by an eddy‐resolving ocean model simulation (OFES). Further analysis demonstrates that seasonal variation of the MC is a component of large‐scale upper‐ocean circulation gyre, while current variations in the MUC layer are confined near the western boundary and featured by shorter‐scale (200–400 km) structures. Most of the MC variations and approximately half of the MUC variations can be explained by the first and second baroclinic modes and caused by local wind forcing of the western Pacific. Semiannual surface wind variability and superimposition of the two baroclinic modes jointly give rise to the enhanced subsurface semiannual variations. The pronounced mesoscale eddy variability in the MUC layer may also contribute to the seasonality of the MUC through eddy‐current interaction.

Historical observations have documented prominent changes of the Mindanao Current (MC) during El Niño events, yet a systematic understanding of how El Niño modulates the MC is still lacking. Mooring observations during December 2010–August 2014 revealed evident year-to-year variations of the MC in the upper 400 m that were well reproduced by the Hybrid Coordinate Ocean Model (HYCOM). Composite analysis was conducted for 10 El Niño events during 1980–2015 using five model-based datasets (HYCOM, OFES, GEOS-ODA, SODA2.2.4, and SODA3.3.1). A consensus is reached in suggesting that a developing (decaying) El Niño strengthens (weakens) the MC, albeit with quantitative differences among events and datasets. HYCOM experiments demonstrate that the MC variability is mainly a first baroclinic mode response to surface wind forcing of the tropical Pacific, but the specific mechanism varies with latitude. The upstream part of the MC north of 7.5°N is controlled by wind forcing between 6° and 9°N through Ekman pumping, whereas its downstream part south of 7.5°N is greatly affected by equatorial winds. Prevailing westerly winds and Ekman upwelling in the developing stage cause cyclonic anomalous circulation in the northwest tropical Pacific that strengthens the MC, and the opposite surface wind forcing effect in the decaying stage weakens the MC. Although ocean models show difficulties in realistically representing the northward-flowing Mindanao Undercurrent (MUC) beneath the MC and its seasonal and interannual variations, all five products suggest an enhancement of the MUC during the decaying stage of El Niño.