Accurate lifetime prediction of transformers operated in power grids with renewable energy systems is a challenging task because it requires a large amount of data that is not usually available. In the case of wind energy, this complexity is intensified with the stochastic ageing process influenced by the intermittency of the wind and weather conditions. Existing models make use of detailed power topologies to evaluate transformer stress profiles and associated degradation. However, this modelling approach requires high computational resources and long simulation times. In this context, this paper presents a lifetime prediction model for transformers designed through probabilistic machine learning, thermal modelling and ageing analysis. The proposed model is compared with synthetic wind-to-power detailed simulations of a wind farm and validated with real data. The lifetime prediction is evaluated with different mission profile estimates and results show that the accuracy of the probabilistic machine learning model is very high, with an error of 0.47% for the median value and 80% prediction interval errors within 6%–7% with respect to observations. Moreover, there is a substantial reduction in the simulation time and memory requirements when compared to the synthetic model. A detailed sensitivity analysis demonstrates the influence on transformer ageing of different overloading strategies, thermal constants and the geographic location of the wind farm.