Thermal management is a key issue for the downsizing of electronic components in order to optimise their performance. These devices incorporate more and more nanostructured materials, such as thin films or nanowires, requiring measurement techniques suitable to characterise thermal properties at the nanoscale, such as Scanning Thermal Microscopy (SThM). In active mode, a hot thermoresistive probe scans the sample surface, and its electrical resistance R changes as a function of heat transfers between the probe and sample. This paper presents the measurement and calibration protocols developed to perform quantitative and traceable measurements of thermal conductivity k using the SThM technique, provided that the heat transfer conditions between calibration and measurement are identical, i.e., diffusive thermal regime for this study. Calibration samples with a known k measured at the macroscale are used to establish the calibration curve linking the variation of R to k. A complete assessment of uncertainty (influencing factors and computational techniques) is detailed for both the calibration parameters and the estimated k value. Outcome analysis shows that quantitative measurements of thermal conductivity with SThM (with an uncertainty value of 10%) are limited to materials with low thermal conductivity (k<10Wm−1K−1).