Viscera and carcasses represent 60–70% of whole fish body weight, and this processing waste is a known source of bioactive molecules, including proteases. These enzymes can be employed in various biotechnological processes, such as, for preparing fish protein hydrolysate (FPH). Therefore, the objective of this study was to evaluate the use of processing waste from Nile tilapia (Oreochromis niloticus) as a source of protein and proteases to produce FPH. Three FPH production conditions were evaluated: two conditions used autolysis with enzymes extracted from the tilapia intestine at different concentrations (FPH100, 100mg of tissue/mL and FPH600, 600mg of tissue/mL) and the third used 0.5% (v/v) Alcalase (FPHcom), a commercial protease preparation. Protein, amino acids and fatty acids content were calculated as DM basis. After a 4-h reaction, maximum hydrolysis percentages from FPHcom, FPH100, and FPH600 systems were 34.73±1.44%, 29.21±0.79%, and 41.66±1.33%, respectively. The protein content in the resulting FPS was 584.8g/kg, 492.3g/kg, and 508.2g/kg for FPHcom, FPH100, and FPH600, respectively. Methionine and lysine were found at levels of 32.0 and 77.0g/kg (FPHcom), 31.0 and 64.0g/kg (FPH100), and 33.0 and 69.0g/kg (FPH600), respectively. Polyunsaturated fatty acid contents of FPHcom, FPH100, and FPH600 were 101.0g/kg, 138.0g/kg, and 70g/kg, respectively, with a predominance of linoleic acid (C18:2n−6). Amino acid composition, lipid profile, and amino acid score suggested that all of the experimental FPHs could be employed as a protein source in diets for aquatic organisms and other farmed animals.