Background and Aims: Fish oil and krill oil are primary sources of Omega-3 polyunsaturated fatty acids (PUFAs), differing in their molecular forms and bioavailability. Understanding these differences can optimize their therapeutic use. This study aims to compare the bioavailability of Omega-3 PUFAs in fish oil and krill oil using a network meta-analysis approach. By evaluating various molecular forms and dosages, the study seeks to identify the most effective Omega-3 sources and dosing regimens to maximize health benefits.Methods: The study adhered to the explanation of the PRISMA network meta-analysis 2015 (registered PROSPERO ID: CRD42024532536). The risk of bias was evaluated using the PEDro scale. This network meta-analysis incorporated data from studies published between 2003 and 2023, sourced from five databases: ClinicalTrials.gov, PubMed, Cochrane CENTRAL, the International Clinical Trials Registry Platform-World Health Organization, and Embase. Statistical analysis was conducted using advanced models in R software to ensure a rigorous evaluation of bioavailability.Results: Out of 26 high-quality studies, findings reveal superior bioavailability of krill oil compared to fish oil. Specifically, fish oil above 3000 mg, in re-esterified triacylglycerol or ethyl ester formulations (100–2900 mg), and krill oil (100–1900 mg) significantly enhanced the Omega-3 index. At lower dosages (under 2000 mg), krill oil shows superior Omega-3 absorption compared to fish oil. Using fish oil ethyl ester at doses between 2000 and 2900 mg may be the most effective for reducing Tmax. However, this finding should be interpreted with caution due to high heterogeneity and limited statistical significance. The highest AUC values were observed in krill oil phospholipid/free fatty acid formulation. Emulsion forms of fish oil are more effective in increasing Cmax than other formulations. These results were supported by robust statistical evidence (Egger's test, p > 0.05), highlighting the effectiveness of specific formulations and doses in optimizing Omega-3 absorption.Conclusion: The research highlights the importance of understanding the bioavailability of Omega-3 PUFAs from fish oil and krill oil. The findings suggest that low-dose krill oil and fish oil emulsions (under 2000 mg) are effective and potentially safer alternatives to high-dose fish oil, potentially minimizing the risk of adverse effects.