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.