A novel two-thermocouple sensor character isation method for use in variable velocity flow environments is described. A difference equation method, recently developed by the authors for constant velo city flow applications, is extended to accommodate variable velocity flows using polynomial parameter fitting on a sliding data window. In particular, by using a novel difference equation formulation the invariance of time-constant ratio with respect to flow velocity is exploited to produce an efficient unbiased and consistent time-constant estimator. Monte-Carlo simulation studies show that the new algorithm outperforms alternatives in the literature without the restrict five requirement of a priori knowledge of thermocouple time constant ratios.