Background: In clinical practice, discordance between anti-müllerian hormone (AMH) and antral follicle count (AFC) presents a recurring challenge. Such discordance can potentially lead to inappropriate clinical decisions, thereby diminishing the clinician’s confidence in managing a patient’s long-term journey through assisted reproductive technology (ART). This study aims to clarify such discordance and identify the more reliable marker between the two, analyzing ART outcomes among Korean infertility patients with AMH and AFC discordance; furthermore, the study elaborates data to evaluate possible patient-related factors contributing to discordance. Methods: This retrospective observational study involved 225 infertile women who underwent their first controlled ovarian stimulation treatment followed by embryo transfer. These patients were categorized into three groups: the congruent (Con) group with predicted AMH according to AFC within 50% prediction interval; the higher-than-predicted (HTP) group with predicted AMH above upper boundary of 50% prediction interval according to AFC; the lower-than-predicted (LTP) group with predicted AMH below lower boundary of 50% prediction interval according to AFC. Variables in the comparative analysis of these three groups focused on ART outcomes. Results: The HTP group which had younger patients with lower dose of follicle stimulation hormone (FSH) achieved better ART outcomes than the LTP group. After adjusting for factors affecting ovarian response such as age, body mass index (BMI), AFC, and total dose FSH usage, the HTP group still demonstrated significantly superior results in terms of the oocyte yield, good-quality embryo rates, and pregnancy rate compared to the LTP group. In the logistic regression analysis, age was not a significant patient factor affecting the ART outcomes; however, the patient’s status of polycystic ovary syndrome (PCOS) was significantly associated with the AMH-AFC discordance, with an odds ratio (OR) of 1.24. Conclusions: Serum AMH provided the more accurate prediction of the patient’s ovarian reserve, especially when the discordance between AMH and AFC was present; more favorable ART outcomes were observed in the patients with the higher AMH measurement than the statistically expected value from their AFC. In addition, the presence of PCOS could be considered as one of the significant factors contributing to such discordance between AMH and AFC.