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Background Varicocoele is the most common correctable cause of male infertility; however, predicting varicocoelectomy outcomes is difficult. “Omics” techniques have been increasingly used to develop new diagnostic and prognostics tools for several male infertility causes, and could be applied to study varicocoele. Objectives The objective is to create metabolomics models capable of segregating men who improved semen analysis (SA) parameters or achieved natural pregnancy after microsurgical varicocoelectomy (MV) from those who did not, using hydrogen‐1 nuclear magnetic resonance (1H NMR) spectra of seminal plasma of pre‐operative samples. Material and methods We recruited 29 infertile men with palpable varicocoele. 1H NMR spectra of seminal plasma were obtained from pre‐operative samples and used to create metabonomics models. Improvement was defined as an increase in the total motile progressive sperm count (TMC) of the post‐operative SA when compared to the baseline, and pregnancy was assessed for 24 months after MV. Results Using linear discriminant analysis (LDA), we created a model that discriminated the men who improved SA from those who did not with accuracy of 93.1%. Another model segregated men who achieved natural pregnancy from men who did not. We identified seven metabolites that were important for group segregation: caprylate, isoleucine, N‐acetyltyrosine, carnitine, N‐acetylcarnitine, creatine, and threonine. Discussion We described the use of metabonomics model to predict with high accuracy the outcomes of MV in infertile men with varicocoele. The most important metabolites for group segregation are involved in energy metabolism and oxidative stress response, highlighting the pivotal role of these mechanisms in the pathophysiology of varicocoele. Conclusions 1H NMR spectroscopy of seminal plasma can be used in conjunction with multivariate statistical tools to create metabonomics models useful to segregate men with varicocoele based on the reproductive outcomes of MV. These models may help counseling infertile men with varicocoele regarding their prognosis after surgery.