Heat-flow data from deep boreholes are of particular value as a number of factors, including climatic surface temperature variations, may disturb subsurface thermal conditions, especially at shallow depths. This study provides thermal results from two boreholes, Gravberg-1 and Stenberg-1, drilled to large depths in the Siljan Ring impact structure, Baltic Shield, Central Sweden. Taking several high-resolution temperature logs to a depth of more than 5000 m in Gravberg-1 and close to 2000 m in Stenberg-1, and up to a long time after drilling, ensures high-quality deep temperature data. A good-quality thermal conductivity profile was determined from mineralogical composition and radiogenic heat production from a spectral gamma-ray log. The observations show overall thermal conductive profiles with local non-conductive temperature variations. Observed present-day near-surface heat flow (depth range 200–500 m) in Gravberg-1 is 47 mW/m2 (std. dev. 1.5 mW/m2). From observed deep background heat flow, considering heat production, the equivalent steady-state, unperturbed heat flow is estimated at 66–68 mW/m2. Data from Stenberg-1 provide similar results. The observed reduction of heat flow at near-surface level by about 20 mW/m2 is interpreted as originating from long-term palaeoclimatic temperature variations. During the last glacial period, the area was, to varying degree, both ice-free and covered by the Fennoscandian ice sheet. Thermal modelling, with a ground-surface mean-temperature increase by 12±2 °C from glacial to post-glacial time, shows consistency between observed and modelled heat flow perturbations for the full depth range of observations. Heat flow perturbations may be significant to depths of about 2000 m. These results show that, uncorrected for palaeoclimate, depending on depths of measurements, observed continental heat flow values might be markedly underestimated. This applies to Northern Europe and, likely, to many other areas as well.