Analysis of results from an eddy-resolving general circulation model showed two subsurface velocity cores in the mean within the depth range between 400 and 1000 m below the Mindanao Current (MC). One is confined to the inshore edge at about 126.8°E and connected with the Sulawesi Sea. The other takes place somewhat offshore around 127.7°E, being closely related to the intrusion of South Pacific water. Both cores are referred to as the Mindanao Undercurrent (MUC). The MC/MUC is approximately a geostrophic flow, except on the inshore edge of the MUC where up to 50% of the mean flow can be explained by ageostrophic dynamics. In contrast with the well-defined southward flowing MC, the MUC is of high velocity variance relative to the mean. Empirical orthogonal function (EOF) analysis shows that approximately 60% of the total velocity variance is associated with two meandering modes, with their major signatures in the subthermocline. The dominant time scale of variability is 50–100 days. An ensemble of these meso-scale fluctuations provides a northward freshwater flux on the offshore edge of the Philippine coast, which to a certain extent explains why water of South Pacific origin appears to extend farther northward than the mean MUC. In the offshore velocity core of the MUC, for example, eddy induced freshwater flux is equivalent to a mean flow of about 0.3 m s−1 in the density range between 26.9 and 27.3 kg m−3, which is greater than the mean current by a factor of 6.