A comprehensive data set collected with the Poker Flat Incoherent Scatter Radar (PFISR) and GPS receiver in Fairbanks, Alaska (magnetic latitude = 65.4°N) in 2007–2010 is employed to analyze and compare the total electron content (TEC) estimates derived from two radio techniques at high latitudes. The average TEC trends are shown to be largely similar and consistent with expectations based on solar conditions. The TEC residuals expressed as the difference and ratio between the PFISR- and GPS-derived TEC are evaluated to be below 2 total electron content units (TECU = 1016 electronsm−2) and 0.7–0.8, respectively, with some dependence on solar conditions. The agreement between TEC estimates is examined by limiting the difference between the GPS satellite and PFISR beam elevations to 2.5° and postintegrating GPS measurements over the period of each PFISR measurement. Factors controlling the agreement are investigated, including possible roles of GPS satellite bias, GPS elevation angle, and topside contribution to TEC. It is demonstrated that the best agreement, expressed as a linear correlation and a fraction of points consistent with the linear trend, is achieved with satellites at the largest elevation angles and smallest distances from PFISR, which are a possible effect of small spatial differences and unremoved differential biases. Estimates of the topside contribution to TEC range between 14% and 30% and are most consistent during daytime hours, while observations near the solar terminator and during the night suffer from large uncertainties.