We present a reconstruction of El Niño Southern Oscillation (ENSO) variability spanning the Medieval Climate Anomaly (MCA, A.D. 800–1300) and the Little Ice Age (LIA, A.D. 1500–1850). Changes in ENSO are estimated by comparing the spread and symmetry of δ18O values of individual specimens of the thermocline-dwelling planktonic foraminifer Pulleniatina obliquiloculata extracted from discrete time horizons of a sediment core collected in the Sulawesi Sea, at the edge of the western tropical Pacific warm pool. The spread of individual δ18O values is interpreted to be a measure of the strength of both phases of ENSO while the symmetry of the δ18O distributions is used to evaluate the relative strength/frequency of El Niño and La Niña events. In contrast to previous studies, we use robust and resistant statistics to quantify the spread and symmetry of the δ18O distributions; an approach motivated by the relatively small sample size and the presence of outliers. Furthermore, we use a pseudo-proxy approach to investigate the effects of the different paleo-environmental factors on the statistics of the δ18O distributions, which could bias the paleo-ENSO reconstruction. We find no systematic difference in the magnitude/strength of ENSO during the Northern Hemisphere MCA or LIA. However, our results suggest that ENSO during the MCA was skewed toward stronger/more frequent La Niña than El Niño, an observation consistent with the medieval megadroughts documented from sites in western North America.