Diminished ovarian reserve (DOR) represents a relevant issue of reproductive medicine that is often associated with infertility and reduced efficacy of IVF programs. The changes in amino acid metabolism can play a role in the DOR pathogenesis as manifestations of the folliculogenesis and oogenesis epigenetic alterations. The study was aimed to assess alterations of amino acid metabolic pathways in blood plasma and follicular fluid and estimate their clinical significance in DOR. A total of 115 infertile women aged 25–42 years were included in the study. Groups were formed based on the ovarian reserve and age. Amino acid levels in blood plasma and follicular fluid were assessed by high performance liquid chromatography–mass spectrometry (HPLC-MS); bioinformatics analysis of amino acid metabolic pathways was performed. We revealed significant changes in the phenylalanine, tyrosine and tryptophan biosynthesis (effect = 0.5; p = 0.026), alanine, aspartate and glutamate metabolism (effect = 0.114; p = 0.013), and arginine biosynthesis (effect = 0.289; p < 0.001) pathways playing a role in folliculogenesis, oogenesis, and embryogenesis. The detected differences in the amino acid levels in various body fluids made it possible to construct the logistic regression models confirming DOR with the 88% probability based on the amino acid levels in follicular fluid (sensitivity 88%, specificity 84%) and 82% probability based on plasma levels (sensitivity 65%, specificity 91%). The findings can be used for further research focused on the pathogenesis of infertility associated with DOR and for selection of the most optimal diagnostic and treatment tactics.