The thermal conductivity λ of plasma enhanced chemical vapor deposited Si3N4 and sputtered AlN thin films deposited on silicon substrates were obtained utilizing the differential 3ω method. A thin electrically conductive strip was deposited onto the investigated thin film of interest, and used as both a heater and a temperature sensor. To study the thickness dependent thermal conductivity of AlN and Si3N4 films their thickness was varied from 300 to 1000 nm. Measurements were performed at room temperature at a chamber pressure of 3.1 Pa. The measured thermal conductivity values of AlN and Si3N4 thin films were between 5.4 and 17.6 Wm− 1 K− 1 and 0.8 up to 1.7 Wm− 1 K− 1, respectively. The data were significantly smaller than that of the bulk materials found in literature (i.e., λAlN = 250–285 Wm− 1 K− 1, λSi3N4 = 30 Wm− 1 K− 1), due to the scaling effects, and also strongly dependent on film thickness, but were comparable with literature for the corresponding thin films.