Background: Bioelectrical impedance analysis (BIA) is a simple and rapid technique to measure body composition (BC). Validity of BIA in patients with low body mass index (BMI) remains controversial. We assessed the validity of several BIA equations to evaluate fat-free mass (FFM), fat mass (FM) and muscle mass in patients with anorexia nervosa (AN) by using dual X ray absorptiometry (DXA) as reference. Methods: Sixteen BIA equations developed for FFM and appendicular lean mass (ALM) were applied on electrical data measured by BIA in AN patients with BMI <16 kg/m². BIA and DXA were done the same day after overnight fasting. Results were compared with the Bland–Altman method, Pearson correlation and a Lin concordance test. Results: Data from 115 female AN patients (14.6 ± 1.2 kg/m²; 32.3 ± 14.5 years) were included. FM and FFM assessed by DXA were, respectively, 4.2 ± 2.4 kg and 35.5 ± 3.8 kg. The best results were obtained with Sun’s equation: respectively for FM and FFM, Bland Altman bias at 0.548 and 0.706 kg, Pearson correlation r at 0.86 and 0.86 and Lin concordance coefficient at 0.81 and 0.84. However, confidence intervals (CI) at 95% were high (−2.73–3.83 kg for FM; −4.55–3.13 kg for FFM). Other equations also showed high 95% CI. Accuracy was acceptable for Sun and Bedogni equations for FFM (approximately 66%) but very low for FM prediction considering all equations (<15%). Concerning ALM evaluated at 14.88 ± 2.04 kg by DXA, only Scafoglieri and Yoshida equations showed acceptable values: bias (−0.2 and 2.8%), Pearson r (0.89 and 0.86), Lin concordance coefficient (0.82 and 0.82) and accuracy (83.5 and 82.6%). Confidence intervals at 95% were high for both equations (−2.1–2.0 for Scafoglieri equation and −1.6–2.4 for Yoshida equation). Conclusion: In AN patients with BMI < 16 kg/m², no BIA equation tested was adapted to evaluate BC at the individual level.