AbstractPacific Decadal Oscillation (PDO) index is an important indicator of climate variability. However, large discrepancies are found among real‐time PDO monitoring indices maintained by several operational centers, with larger uncertainty exhibiting prior to 1950s and after late 1990s on seasonal to decadal time scales. Two historical sea surface temperature (SST) data sets are used to investigate causes for the uncertainty: the Extended Reconstructed Sea Surface Temperature version 3b (ERSST 3b) and the Hadley Center Sea Ice and SST data set (HadISST) version 1. It is found that choices of spatial structure of Empirical Orthogonal Function (EOF) vector and SST data set are important sources of uncertainty on seasonal to decadal time scales, while choice of climatological base period only contributes to uncertainty on seasonal time scale. Decadal variation of differences in PDO indices from ERSST and HadISST is associated with systematic differences between the two data sets in the central and the north‐eastern Pacific.