Both the growing prevalence of chronic diseases and the consumer's health awareness have increased the intake of fish oil supplements since it is rich in omega-3. However, the proposed preventive or therapeutic effects of fish oil in different diseases are inconsistent, partially because processing affects on omega-3 stability and bioavailability. Thus, this review aims to describe the influence of fish oil processing on the omega-3 bioavailability in humans. This review illustrates how fish oil is obtained and processed, summarizes how omega-3 bioavailability is assessed, and describes how the molecular form and formulation may modulate their bioavailability. The bioavailability of omega-3 depends on the processing and formulation of fish oil, which influences the acceptability and stability of the final product. Currently, omega-3 is more bioavailable when ingested as free fatty acid, followed by triglyceride, and lastly as ethyl ester. Due to their high susceptibility to oxidation and preliminary findings, administering omega-3 in the form of triglyceride may be the most suitable to maximize bioavailability. Additionally, formulations that promote self-emulsification of fish oil show promise, though more human studies are needed to support these results. These results could optimize the bioavailability of omega-3 and the potential health-related applications of fish oil.