We demonstrate the use of transient IR absorption measurements for picosecond thermometry of protein in an aqueous environment. For small temperature changes, measured transient absorption changes are shown to be in excellent agreement with the "static" temperature dependence of the protein and water constituents of the sample as measured by FTIR spectroscopy. The thermally induced changes in IR absorption reach equilibrium within a few picoseconds, making this technique an excellent tool for picosecond thermometry.