The use of complementary herbal medicines has recently increased in an attempt to find effective alternative therapies that reduce the adverse effects of chemical drugs. Portulacaria afra is a rich source of phytochemicals with high antioxidant activity, and thus may possess health benefits. This study used the latest developments in GC-MS coupling with molecular docking techniques to identify and quantify the phytoconstituents in P. afra tissue extracts. The results revealed that n-butanol P. afra (BUT-PA) dry extracts contained total phenolic and flavonoids contents of 21.69 ± 0.28 mgGAE/g and 196.58 ± 6.29 mgGAE/g, respectively. The significant potential of antioxidants was observed through CUPRIC, FRAP, and ABTS methods while the DPPH method showed a moderate antioxidants potential for P. afra. Enzymatic antioxidants, superoxide dismutase, peroxidase and catalase also showed a better response in the BUT-PA dry extracts. The thrombolytic activity of the BUT-PA extracts ranged from 0.4 ± 0.32 to 11.2 ± 0.05%. Similarly, hemolytic activity ranged from 5.76 ± 0.15 to 9.26 ± 0.15% using the standard (triton x) method. The BUTPA and CHPA showed moderate acetylcholinesterase and butrylcholinesterase inhibition, ranging from 40.78 ± 0.52 to 58.97 ± 0.33, compared to galantamine. The carrageenan induced hind-paw edema assay, while BUT-PA extracts showed anti-inflammatory properties in a dose-dependent manner. Furthermore, 20 compounds were identified in the BUTPA extracts by GC-MS. Molecular docking was performed to explore the synergistic effect of the GC-MS-identified compounds on COX-1 and COX-2 inhibition. A high binding affinity was observed for Stigmastan-3, 5-diene, Phthalic acid, 3. Alpha-Hydroxy-5, 16-androstenol. The computed binding energies of the compounds revealed that all the compounds have a synergistic effect, preventing inflammation. It was concluded that active phytochemicals were present in P. afra, with the potential for multiple pharmacological applications as a latent source of pharmaceutically important compounds. This should be further explored to isolate secondary metabolites that can be employed in the treatment of different diseases.