Pre-cooked bone is a waste product generated during tuna processing and can serve as a potential source of biocalcium (BC). Generally, non-collagenous protein and fat must be removed properly from bone. A NaCl solution can be used to remove such proteins, while fish lipase can be used in a green process, instead of solvent, for fat removal. Thus, this study aimed to investigate the impact of NaCl pretreatment at different concentrations in combination with heat to eliminate non-collagenous proteins, and to implement fish lipase treatments at varying levels for fat removal, for BC production from pre-cooked tuna bone. Optimal NaCl pretreatment of bone was achieved when a 5% NaCl solution at 80 °C was used for 150 min. The lowest lipid content was obtained for bone defatted with crude lipase extract (CLE) at 0.30 Unit/g of bone powder for 2 h. BC powder from bone defatted with CLE (DF-BC) possessed greater contents of ash, calcium, and phosphorus and smaller particle sizes than the control BC powder. X-ray diffractograms suggested that both BC powders consisted of hydroxyapatite as a major compound, which had a crystallinity of 62.92–63.07%. An elemental profile confirmed the presence of organic and inorganic matter. Thus, BC powder could be produced from pre-cooked tuna bone using this ‘green process’.