Seeds and fruits of Citrullus colocynthis have been reported to possess huge potential for the development of phytopharmaceuticals with a wide range of biological activities. Thus, in the current study, we are reporting the potential antimicrobial and anticancer properties of C. colocynthis seeds extracted with solvents of different polarities, including methanol (M.E.), hexane (H.E.), and chloroform (C.E.). Antimicrobial properties of C. colocynthis seeds extracts were evaluated on Gram-positive and Gram-negative bacteria, whereas, anticancer properties were tested on four different cell lines, including HepG2, DU145, Hela, and A549. All the extracts have demonstrated noteworthy antimicrobial activities with a minimum inhibitory concentration (MIC) ranging from 0.9–62.5 µg/mL against Klebsiella planticola and Staphylococcus aureus; meanwhile, they were found to be moderately active (MIC 62.5–250 µg/mL) against Escherichia coli and Micrococcus luteus strains. Hexane extracts have demonstrated the highest antimicrobial activity against K. planticola with an MIC value of 0.9 µg/mL, equivalent to that of the standard drug ciprofloxacin used as positive control in this study. For anticancer activity, all the extracts of C. colocynthis seeds were found to be active against all the tested cell lines (IC50 48.49–197.96 µg/mL) except for the chloroform extracts, which were found to be inactive against the HepG2 cell line. The hexane extract was found to possess the most prominent anticancer activity when compared to other extracts and has demonstrated the highest anticancer activity against the DU145 cell line with an IC50 value of 48.49 µg/mL. Furthermore, a detailed phytoconstituents analysis of all the extracts of C. colocynthis seeds were performed using GC–MS and GC–FID techniques. Altogether, 43 phytoconstituents were identified from the extracts of C. colocynthis seeds, among which 21, 12, and 16 components were identified from the H.E., C.E., and M.E. extracts, respectively. Monoterpenes (40.4%) and oxygenated monoterpenes (41.1%) were the most dominating chemical class of compounds from the hexane and chloroform extracts, respectively; whereas, in the methanolic extract, oxygenated aliphatic hydrocarbons (77.2%) were found to be the most dominating chemical class of compounds. To the best of our knowledge, all the phytoconstituents identified in this study are being reported for the first time from the C. colocynthis.