BackgroundStudying the relationships between rapeseed seed yield (SY) and its yield-related traits can assist rapeseed breeders in the efficient indirect selection of high-yielding varieties. However, since the conventional and linear methods cannot interpret the complicated relations between SY and other traits, employing advanced machine learning algorithms is inevitable. Our main goal was to find the best combination of machine learning algorithms and feature selection methods to maximize the efficiency of indirect selection for rapeseed SY.ResultsTo achieve that, twenty-five regression-based machine learning algorithms and six feature selection methods were employed. SY and yield-related data from twenty rapeseed genotypes were collected from field experiments over a period of 2 years (2019–2021). Root mean square error (RMSE), mean absolute error (MAE), and determination coefficient (R2) were used to evaluate the performance of the algorithms. The best performance with all fifteen measured traits as inputs was achieved by the Nu-support vector regression algorithm with quadratic polynomial kernel function (R2= 0.860, RMSE = 0.266, MAE = 0.210). The multilayer perceptron neural network algorithm with identity activation function (MLPNN-Identity) using three traits obtained from stepwise and backward selection methods appeared to be the most efficient combination of algorithms and feature selection methods (R2= 0.843, RMSE = 0.283, MAE = 0.224). Feature selection suggested that the set of pods per plant and days to physiological maturity along with plant height or first pod height from the ground are the most influential traits in predicting rapeseed SY.ConclusionThe results of this study showed that MLPNN-Identity along with stepwise and backward selection methods can provide a robust combination to accurately predict the SY using fewer traits and therefore help optimize and accelerate SY breeding programs of rapeseed.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13007-023-01035-9.