Measurement uncertainties of a CMOS-based piezoresistive stress sensor are studied for low cycle thermal loading applications. After the fundamentals of the sensor are reviewed briefly, the random uncertainties associated with the data acquisition unit are evaluated first using raw current signals obtained from uniquely fabricated free-standing stress sensor chips. The free-standing sensor chips are tested further for systematic uncertainties associated with the manufacturing-induced residual stresses by subjecting them to a thermal cycle. Finally, the stress measurement accuracy of the sensor chip under an in-situ thermal loading is quantified by a numerical model verified by a sub-micron sensitivity optical technique while incorporating the quantified uncertainties.