We present a simple method for simultaneous measurement of thermo-optic and stress-optic coefficients of polymer thin films by measuring the film refractive indices as a function of temperature ( $\mathrm{d}n/\mathrm{d}T$ ). Usually, such $\mathrm{d}n/\mathrm{d}T$ value is considered as the thermo-optic coefficient. However, in the thin film systems, the measured $\mathrm{d}n/\mathrm{d}T$ values result from both the thermo-optic and stress-optic effects. To demonstrate the stress-induced effects, the $\mathrm{d}n/\mathrm{d}T$ values have been investigated for two different polymers: benzocyclobutene (high film stress) and epoxy 3505 (negligible film stress), using a prism coupler technique. The finite element method has been used so as to predict the stresses in the polymer film and, by combining them with the experimental $\mathrm{d}n/\mathrm{d}T$ values, the individual thermo-optic and stress-optic coefficients have been determined. We found that the obtained thermo-optic coefficient is significantly different than the measured $\mathrm{d}n/\mathrm{d}T$ values. The method is generic in nature and can thus be applied to a wide range of polymer waveguide materials.