Citrulline is a non-protein building amino acid that plays important roles in nitric oxide production, vasodilation and ammonia detoxification. It is structurally related to arginine and is most abundant in melons and other cucurbit species. Most current methods for the quantification of citrulline and arginine require time-consuming chemical derivatization steps, and often use more expensive detection methods such as fluorescence detection. Hence, this study aimed to develop a simple and rapid reversed-phase high-performance liquid chromatography method using ultraviolet detection (RP-HPLC–UV), without requiring any analyte derivatization. The method was used to quantify the citrulline and arginine content of 13 Australian fruit and vegetable cultivars, comprising 11 species from 7 genera and 5 families. The highest citrulline contents were found in mature citron melon (Citrullus lanatus var. citroides) fruit (39.2 mg/g dry weight basis), which also had the highest citrulline: arginine ratio of 17.8. Red watermelon (Citrullus lanatus) flesh also contained high levels of citrulline (22.9 mg/g), with lower concentrations in other melons, pumpkin and squash (1–3 mg/g). Arginine levels were highest in red watermelon flesh (8.1 mg/g). This extraction protocol and HPLC method may be suitable for screening large number of samples for citrulline and arginine contents.