The vertically integrated horizontal energy transports and the vertically integrated vertical energy flux divergence from ERA-40 and ISCCP are not in balance assuming a stationary climate as a time mean over several years. The reasons are the inherent uncertainties in each of the respective data sets. We therefore modify them using a variational approach with a discretization in spherical harmonics to obtain consistent values. The variational approach only modifies the smaller yet more uncertain divergent part of the flow, leaving the large rotational part untouched. From these consistent fields we can calculate posterior covariance matrices of the vertically integrated horizontal energy transport and the vertically integrated vertical energy flux divergence, providing a measure of the uncertainty of the previous calculation. We are able to use these posterior covariance matrices to give an estimate of the uncertainty of the zonally and vertically integrated meridional energy transport, which is about 0.25 PW in the tropics and 0.04 PW in high latitudes, as well as for the vertical energy flux divergence of the atmosphere, which ranges from 2.5 to 5 W/m2 in the tropics to 15–17 W/m2 in high latitudes.