Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is a cucurbit with high value in Burkina Faso. It is appreciated for its fruits, which are widely consumed. In the literature, watermelon is described as an important source of bioactive compounds beneficial to health. There is very little scientific data on this supposed nutraceutical potential of the watermelon. This study aimed to characterize the nutraceutical and antioxidant potential of the pulp of five watermelon cultivars grown in Burkina Faso to identify the best cultivars for consumers. The study focused on the physicochemical, nutraceutical, and antioxidant activity characterization of the cultivars using standard methods. This study revealed a significant variation in total phenolics, flavonoids, β-carotene, and lycopene contents between the five cultivars while the color did not show significant variation. The color parameters with ΔE ranging from 40.62 ± 4.87 (SB cultivar) to 48.90 ± 15.81 (KK cultivar) determined did not reveal any significant difference between cultivars. For the phytochemical parameters: total phenolic compounds, total flavonoids, β-carotene, and lycopene, the cultivars KK and KA showed the highest content. The statistical analysis of the results shows positive correlations between phytochemical composition and pulp color. The color could thus, depending on the cultivar and its maturity, constitute a preliminary indicator of choice for the estimation of the content of bioactive compounds.