17α-methyltestosterone (MT) is a synthetic steroid used to induce masculinization when administered during the larval stage of fish. However, the side effects of MT on eel are still poorly understood and, in this study, we examined the various effects of MT on juvenile eel A. japonica (100.63 ± 8.56 mm total length (TL)). To further investigate growth and sex differentiation, juvenile eels (n = 1000) were exposed to 25 µg/g MT for 6 months. We analyzed growth-related factors, sex steroid hormones, skin pigmentation, and color-related gene expression. Through this study, we found a 90% sex conversion of juvenile eels to males using MT treatment. In the MT-treated eel group (285.97 ± 26.21 mm TL) where sexual maturity was induced, spermatogonia stages were observed in the gonads. In contrast, the control group (395.97 ± 27.72 mm TL) exhibited an 80% immaturity rate, with only 20% of the subjects that were rapidly developing displaying early oogonia. ELISA analysis results showed that the level of growth hormone, which is known to be secreted from spermatogonia, did not change as a result of MT treatment. We confirmed that MT delayed growth and caused morphological changes, particularly a shortened snout length and pigmentation of the fin. The total length, body weight, and snout length were considerably lower in the experimental group than in the control group. In addition, in histological analysis we also observed that some of the MT-treated group (5 out of 10 fish) showed liver atrophy and inflammation, and physiological analysis showed that the cortisol concentration increased in the MT-treated eels. Interestingly, we found that some pigment color-related genes, such as melanocortin 1 receptor (MC1R), tyrosinase (Tyr), and dopachrome tautomerase (DCT), were significantly overexpressed in the fins of MT-treated eels. These results suggest that the treatment of A. japonica larvae with MT induced masculinization but also causes growth side effects from the use of synthetic hormones.