The surface energy balance is a key factor influencing the ground thermal regime. With ongoing climate change, it is crucial to understand the interactions of the individual heat fluxes at the surface and within the subsurface layers, as well as their relative impacts on the permafrost thermal regime. A unique set of high-altitude meteorological measurements was analysed to determine the energy balance at three mountain permafrost sites in the Swiss Alps (Murtèl–Corvatsch, Schilthorn and Stockhorn), where data have been collected since the late 1990s in the framework of the Swiss Permafrost Monitoring Network (PERMOS). All stations are equipped with sensors for four-component radiation, air temperature, humidity, and wind speed and direction, as well as ground temperatures and snow height. The three sites differ considerably in their surface and ground material composition, as well as their ground ice contents. The energy fluxes were calculated based on two decades of field measurements. While the determination of the radiation budget and the ground heat flux is comparatively straightforward (by the four-component radiation sensor and thermistor measurements within the boreholes), larger uncertainties exist for the determination of turbulent sensible and latent heat fluxes. Our results show that mean air temperature at Murtèl–Corvatsch (1997–2018, 2600 m a.s.l.) is −1.66 ∘C and has increased by about 0.8 ∘C during the measurement period. At the Schilthorn site (1999–2018, 2900 m a.s.l.) a mean air temperature of −2.60 ∘C with a mean increase of 1.0 ∘C was measured. The Stockhorn site (2003–2018, 3400 m a.s.l.) recorded lower air temperatures with a mean of −6.18 ∘C and an increase of 0.5 ∘C. Measured net radiation, as the most important energy input at the surface, shows substantial differences with mean values of 30.59 W m−2 for Murtèl–Corvatsch, 32.40 W m−2 for Schilthorn and 6.91 W m−2 for Stockhorn. The calculated turbulent fluxes show values of around 7 to 13 W m−2 using the Bowen ratio method and 3 to 15 W m−2 using the bulk method at all sites. Large differences are observed regarding the energy used for the melting of the snow cover: at Schilthorn a value of 8.46 W m−2, at Murtèl–Corvatsch 4.17 W m−2 and at Stockhorn 2.26 W m−2 are calculated, reflecting the differences in snow height at the three sites. In general, we found considerable differences in the energy fluxes at the different sites. These differences help to explain and interpret the causes of a warming atmosphere. We recognise a strong relation between the net radiation and the ground heat flux. Our results further demonstrate the importance of long-term monitoring to better understand the impacts of changes in the surface energy balance components on the permafrost thermal regime. The dataset presented can be used to improve permafrost modelling studies aiming at, for example, advancing knowledge about permafrost thaw processes. The data presented and described here are available for download at the following site: https://doi.org/10.13093/permos-meteo-2021-01 (Hoelzle et al., 2021).