Background: The homeopathic complex HomeoAqua Mega 3® was designed to stimulate fish liver function resulting in enhanced lipid metabolism and improved overall performance. The effect of the complex in fatty acid compounds in the muscle tissues and the performance of Nile tilapia (O. niloticus) were evaluated.Methods: A control diet with 40 mL of alcohol solution (30° Gay Lussac (GL) alcohol) per kg of feed and another diet with 40 mL/kg of the homeopathic complex were analysed in sex-reversed juvenile male Nile tilapia with mean initial weights of 89.54 g (±7.97) and 89.74 g (±8.83) and initial total mean lengths of 16.93 cm (±0.56) and 16.85 cm (±0.56) for the control and homeopathy-treated fish, respectively. Overall, 200 fish were distributed into 10 water tanks, with 20 specimens in each 600 L tank, they were kept for 63 days. Monitoring of the water’s physical and chemical parameters was performed. Additionally, the percentage chemical composition and the composition of the muscle tissue fatty acids were determined, and fish performance was evaluated.Results: No significant differences (p > 0.05) were found between treatments with regard to the water’s physical and chemical parameters, moisture, ashes, proteins of the Nile tilapia muscular tissue and mean rates of total weight and length of the animals in the final period of the assay. The total lipid (TL) rates of the tilapia muscle tissue were 1.133 ± 0.2% at the start (control and homeopathy) and 0.908 ± 0.14% (control) and 0.688 ± 0.14% (homeopathy) at the end of the experiment (p < 0.06). The sum total of the SFAs (saturated fatty acids) was 338.50 ± 0.15 at the start (control and homeopathy) and 271.49 ± 0.34 mg/g of the TLs for the control and 226.12 ± 0.77 mg/g of TL for the homeopathy at the end of the experiment (p < 0.05). The n−6/n−3 ratio was also lower for the homeopathy-treated fish (8.45 ± 0.40) compared with the control fish (9.60 ± 0.14), (p < 0.05) at the end of the 63-day period.Conclusion: Nile tilapia juveniles that received the HomeoAqua Mega-3® in their diets had a decrease in the TL rates, mainly for the SFAs, and the n−6/n−3 ratio, compared with the control group, without any changes in the animal performance during the experimental period.