Hypericum lanuginosum is one of the traditional medicinal plants that grows in the arid area of the Al-Naqab desert in Palestine and is used by Bedouins to heal various communicable and non-communicable illnesses. The purpose of this investigation was to estimate the total phenolic, flavonoid, and tannin contents of aqueous, methanol, acetone, and hexane H. lanuginosum extracts and evaluate their cytotoxic, anti-oxidative, and antimicrobial properties. Qualitative phytochemical tests were used to identify the major phytochemical classes in H. lanuginosum extracts, while total phenol, flavonoid, and tannin contents were determined using Folin–Ciocalteu, aluminum chloride, and vanillin assays, respectively. Moreover, a microdilution test was employed to estimate the antimicrobial activity of H. lanuginosum extracts against several microbial species. At the same time, the cytotoxic and free radical scavenging effects were evaluated using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) and 2, 2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) assays, respectively. Quantitative examinations showed that the highest amounts of phenols, flavonoids, and tannins were noticed in the H. lanuginosum aqueous extract. Moreover, H. lanuginosum aqueous extract showed potent activity against methicillin-resistant Staphylococcus aureus even more than Amoxicillin and Ofloxacin antibiotics, with Minimum Inhibitory Concentrations (MICs) of 0.78 ± 0.01, 0, and 1.56 ± 0.03 µg/mL, respectively. Additionally, the aqueous extract exhibited the highest activity against Candida albicans and Epidermatophyton floccosum pathogens, with MIC values of 0.78 ± 0.01 µg/mL. Actually, the aqueous extract showed more potent antimold activity than Ketoconazole against E. floccosum with MICs of 0.78 ± 0.01 and 1.56 ± 0.02 µg/mL, respectively. Furthermore, all H. lanuginosum extracts showed potential cytotoxic effects against breast cancer (MCF-7), hepatocellular carcinoma (Hep 3B and Hep G2), and cervical adenocarcinoma (HeLa) tumor cell lines. In addition, the highest free radical scavenging activity was demonstrated by H. lanuginosum aqueous extract compared with Trolox with IC50 doses of 6.16 ± 0.75 and 2.23 ± 0.57 µg/mL, respectively. Studying H. lanuginosum aqueous extract could lead to the development of new treatments for diseases such as antibiotic-resistant microbes and cancer, as well as for oxidative stress-related disorders such as oxidative stress. H. lanuginosum aqueous extract may help in the design of novel natural preservatives and therapeutic agents.