Methods and systems for precise temperature and timebase ppm error estimation using multiple timebases may comprise measuring a temperature corresponding to the plurality of timebases. The frequencies of the timebases may be compared to generate error functions for the timebases, and generating a more accurate reading of the temperature based, at least in part, on the measured temperature and the error functions for the timebases. The timebases may be calibrated utilizing the generated more accurate reading. The plurality of timebases may comprise different order temperature dependencies. The models of temperature dependencies of each of the plurality of timebases may be updated based, at least in part, on the fine reading of the temperature corresponding to the plurality of timebases. A global navigation satellite system (GNSS) clock signal may be utilized periodically to improve the accuracy of the calibration of the plurality of timebases.