With the growing use of anti-obesity medications (AOMs), particularly glucagon-like peptide-1 (GLP-1) receptor agonists, interest in their impact on chemosensory function has increased. We report a case of subjective olfactory discomfort that developed during AOM therapy despite normal objective test results. A 41-year-old woman received the GLP-1 receptor agonist semaglutide for 24 weeks. Thorough olfactory function evaluation was performed using the Questionnaire of Olfactory Disorders (a validated questionnaire), the Yonsei Olfactory Function Test (for psychophysical testing), and chemical gustometry. The tests were performed before treatment and after 24 weeks of AOM therapy. At baseline, the patient had no olfactory complaints and showed normal test results. After treatment, she reported significant subjective olfactory discomfort (visual analog scale score: 48, maximum: 50), with decreased quality of life and parosmia, despite stable Yonsei Olfactory Function scores and normal gustatory function. This case highlights the possible mismatch between subjective and objective olfactory assessment during AOM therapy. Comprehensive chemosensory evaluations and interdisciplinary collaboration are essential, and further large-scale long-term studies are required.