The excellent mechanical properties of thin film shape memory alloys like Nickel-Titanium (NiTi) have led to their widespread use in MEMS-based micropumps, microactuators, microgrippers, etc. Shape memory based micropumps and actuators have superior work densities compared to other technologies. Characterization of thermophysical properties of these materials is important for modeling the behavior of NiTi-based microdevices. For example, the frequency response of shape-memory based microactuators depends on the rate of dissipation of thermal energy, which is a strong function of the thermal properties of the thin film. While bulk thermal properties of NiTi have been reported before, there exists very little work on measuring these properties for the thin film form. This paper uses the 3-ω method for measurement of thermal conductivity of NiTi thin films. NiTi is sputtered on a Silicon substrate, followed by patterning of a metal heater line. Front-to-backside alignment and Deep Reactive Ion Etching (DRIE) of the substrate results in a free standing thin film of NiTi. A sinusoidal electric current is passed through the metal heater, and the third harmonic of the voltage is measured using a lock-in amplifier. This is used to determine the temperature oscillation in the metal heater, which provides the thin film thermal conductivity using a recently developed analytical model for 3-ω measurements in a two-dimensional free standing thin film. The measured values are found to be much lower than the known bulk thermal conductivity of NiTi. This highlights the importance of thin film property measurements instead of using bulk properties. Data obtained in this work is likely to be useful for improved modeling of thin film shape memory based microdevices.