Background: Watermelon (Citrullus lanatus) seed is one of the underutilized crops in Africa. It is a valuable food resource but its usage is limited due to the presence of anti-nutritional factors and its poor storage properties. In this study, the comparative effect of processing methods on nutritional, anti-nutritional and functional properties of watermelon seed flour was determined. Methods; Watermelon seeds were subjected to different processing methods (soaking, germination and boiling), dried and milled into flours. Proximate composition, antinutritional factors (tannins, phytates, oxalate, saponins, trypsin inhibitor, and glycogenic glycoside) and functional properties (water and oil absorption capacity, bulk density, foaming capacity) of the flour were determined using standard methods and analytical procedures. Results: There were significant differences (p<0.05) in the proximate contents between different processing methods. The value of protein content of the seed flours ranges from 13.25±1.70–18.77±0.63 %. All the anti-nutritional factors were significantly reduced (p<0.05) in the processed seed flour when compared to the unprocessed seeds flour. Soaking significantly (p0.05) was seen in arginine, methionine, proline and aspartic acid of all the seed flours. The processed seed flour also exhibited desirable functional properties when compared with the unprocessed seed flour. Conclusion: Soaking, germination and boiling can be used for the reduction of antinutrient contents while improving the nutrient density and bioavailability of water-melon seed flour. Thus the processed seed flour hence may be useful for confectionery products, aerated foods and high nutrient density weaning foods.