(1) Background: We hypothesized that female sex would have a differential impact on left atrial (LA) low-voltage areas (LVAs) according to CHA(2)DS(2)-VA scores. (2) Methods: This study included 553 patients who underwent radiofrequency catheter ablation (RFCA) for atrial fibrillation (AF). LVAs were defined as regions with bipolar peak-to-peak voltages of <0.5 mV. The proportion of LVAs was calculated by dividing the total LVA by the LA surface area. (3) Results: There was no sex-related difference in LA LVAs among patients with a CHA(2)DS(2)-VA scores /= 30%). Females had odd ratios of 27.82 (95% confidence interval (CI) 3.33-756.8, p = 0.01), and 1.53 (95% CI 0.81-2.83, p = 0.184) for extensive LAVs in patients with CHA(2)DS(2)-VA scores >/= 3 and CHA(2)DS(2)-VA scores < 3, respectively. In the multiple regression model, female patients with a CHA(2)DS(2)-VA >/=3 were significantly associated with a higher proportion of LVAs (beta = 8.52, p = 0.039). (4) Conclusions: Female sex was significantly associated with extensive LVAs, particularly when their CHA(2)DS(2)-VA scores were >/=3. This result suggests that female sex has a differential effect on the extent of LVAs based on the presence of additional risk factors.