Two subsurface moorings were deployed east of Mindanao Island, the Philippines, at 7°01′N, 126°55′E and 7°01′N, 127°46′E, at the location of the inshore and offshore cores of the Mindanao Undercurrent (MUC) suggested by past studies, from September 2011 to October 2012 and March 2013. A steady northward undercurrent, the MUC, was not confirmed by these observations, not only at the location of its inshore core but also of the offshore core. The observed mean flow at the mooring sites seems to be part of an anticyclonic eddy rather than the MUC. A particle‐tracking experiment using a high‐resolution general circulation model output showed that the northward mean flow, called the MUC by past studies, was too weak to advect water to the north. The Mindanao Current during 2011–2012 was weaker than during 1999–2002 because the sea surface height in the Philippine Sea during 2011–2012 was lower than that during 1999–2002. Intraseasonal variability with periods of 50–100 days was observed at the mooring sites, comparable to the previous observations during 1999–2002. Westward signal propagations were observed with periods and speeds of 50 days and 0.20 m s−1 at 300 m depth and of 60–72 days and 0.11–0.14 m s−1 at 960 m depth.