To improve the commercial value of underutilized fish-trade by-products, immunomodulatory peptides were detected and subsequently isolated from the trypsin hydrolysate of tuna trimmings. The gel-isolated fraction T1 of the hydrolysate showed the best enhancement of immune activity. The addition of T1 to RAW264.7 cells enhanced phagocytosis and promoted the secretion of NO, IL-1β, IL-6 and TNF-α. Moreover, T1 significantly accelerated the expression of TLR2 and TLR4, promoted the phosphorylation of IKK and p65, and further activated the NF-κB signalling pathway to promote the immune response of RAW264.7 cells. By analyzing computer-simulated docking with TLR2 and TLR4, key immunomodulatory peptides were identified. The immune activity of synthetic peptides was verified, with HIAEEADRK and AEQAESDKK exhibiting the strongest immune activity. Ultimately, the T1 fraction demonstrated the most potential as an immune-enhancing source of nutraceutical and functional foods, and peptides HIAEEADRK and AEQAESDKK were the potential bioactive ingredient of the T1 fraction.