Lactate threshold is considered an essential parameter when assessing performance of elite and recreational runners and prescribing training intensities in endurance sports. However, the measurement of blood lactate concentration requires expensive equipment and the extraction of blood samples, which are inconvenient for frequent monitoring. Furthermore, most recreational runners do not have access to routine assessment of their physical fitness by the aforementioned equipment so they are not able to calculate the lactate threshold without resorting to an expensive and specialized centre. Therefore, the main objective of this study is to create an intelligent system capable of estimating the lactate threshold of recreational athletes participating in endurance running sports. The solution here proposed is based on a machine learning system which models the lactate evolution using recurrent neural networks and includes the proposal of standardization of the temporal axis as well as a modification of the stratified sampling method. The results show that the proposed system accurately estimates the lactate threshold of 89.52% of the athletes and its correlation with the experimentally measured lactate threshold is very high (R=0,89). Moreover, its behaviour with the test dataset is as good as with the training set, meaning that the generalization power of the model is high. Therefore, in this study a machine learning based system is proposed as alternative to the traditional invasive lactate threshold measurement tests for recreational runners.