Anthropogenic chemicals as emerging contaminants, such as pharmaceuticals, increased worldwide in the environment. This study aimed to apply metabolomics-based approaches on the fish model species three-spined stickleback (Gasterosteus aculeatus) exposed to diclofenac (DCF) to identify toxicity pathways and potential biomarkers. For this purpose, males and females were exposed to a continuous flow of diclofenac solution in laboratory for 21 days, followed by 3 days of depuration, to nominal concentrations of 1 (low) and 100 µg/L (high) of DCF. A methodology based on liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) was employed. Uni-and multivariate statistical analyses were combined to evaluate the modulations of the liver metabolome of G. aculeatus after exposure to DCF. The metabolomics data revealed variations both as a function of time and of the DCF concentration. We observed 2487 altered metabolites, with 1460 and 1027 specific to males and females, respectively. Some of them were significantly impaired by the experimental conditions. However, we showed that several metabolites were impacted by other factors as they were already modulated in the control individuals. The results indicated that the energy metabolism was up-modulated in females and down-modulated in males, with the presence of DCF. The antioxidant system was impacted in males, suggesting oxidative stress in the metabolism, while the immunity system was down-regulated in females following exposure. Moreover, our results revealed 1 and 4 metabolites as potential metabolic biomarkers in male and female sticklebacks, respectively. Among them, the glutaryl-carnitine and the adipoylcarnitine were putatively identified in females, known to be implicated in the energy metabolism. These 5 metabolites showed to be promising biomarkers since they were early modulated during exposure to the stress and showed a notable trend through time.