We explore a supervised machine learning approach to estimate the entanglement entropy of multi-qubit systems from few experimental samples. We put a particular focus on estimating both aleatoric and epistemic uncertainty of the network’s estimate and benchmark against the best known conventional estimation algorithms. For states that are contained in the training distribution, we observe convergence in a regime of sample sizes in which the baseline method fails to give correct estimates, while extrapolation only seems possible for regions close to the training regime. As a further application of our method, highly relevant for quantum simulation experiments, we estimate the quantum mutual information for non-unitary evolution by training our model on different noise strengths.