The validation of sea surface temperature (SST) retrieved from the new sensor Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-Orbiting Partnership (S-NPP) Satellite is essential for the interpretation, use, and improvement of the new generation SST product. In this study, the magnitude and characteristics of uncertainties in S-NPP VIIRS SST produced by the Naval Oceanographic Office (NAVO) are investigated. The NAVO S-NPP VIIRS SST and eight types of quality-controlled in situ SST from the National Oceanic and Atmospheric Administration in situ Quality Monitor (iQuam) are condensed into a Taylor diagram. Considering these comparisons and their spatial coverage, the NAVO S-NPP VIIRS SST is then validated using collocated drifters measured SST via a three-way error analysis which also includes SST derived from Moderate Resolution Imaging Spectro-radiometer (MODIS) onboard AQUA. The analysis shows that the NAVO S-NPP VIIRS SST is of high accuracy, which lies between the drifters measured SST and AQUA MODIS SST. The histogram of NAVO S-NPP VIIRS SST root-mean-square error (RMSE) shows normality in the range of 0–0.6 °C with a median of ~0.31 °C. Global distribution of NAVO VIIRS SST shows pronounced warm biases up to 0.5 °C in the Southern Hemisphere at high latitudes with respect to the drifters measured SST, while near-zero biases are observed in AQUA MODIS. It means that these biases may be caused by the NAVO S-NPP VIIRS SST retrieval algorithm rather than the nature of the SST. The reasons and correction for this bias need to be further studied.