Munronia pinnata (Bin kohomba) and Andrographis paniculata (Heen Binkohomba) are two medicinal plants naturally distributed in a wide variety of habitats in Sri Lanka. They have been widely used in traditional medicine. Both plant species are known to have anti-inflammatory properties. However, drug-target interaction patterns of chemical constituents in both plants necessary to optimize targeted drug activity are yet to be studied. Hence, the objective of this investigation was to assess the molecular interaction between phytocompounds from both plants and one of the most prevalent target proteins of anti-inflammatory medications through molecular docking. The chosen phytocompounds were subjected to docking with the cyclo-oxygenase-1 protein target using Auto Dock Vina 1.2.0 to determine their binding affinity values in comparison to the native ligand, Indomethacin. Ligand-based pharmacokinetics, target prediction, and toxicity prediction were assessed using online tools such as SwissADME, Swiss Target Prediction, and pkCSM. The findings demonstrated that the chemical compound with the highest binding affinity in Binkohomba was Campesterol (-8.3 kcal/mol), while in Heen Binkohomba, it was 7-O-Methylwogonin with a binding affinity of -8.8 kcal/mol. Both chemical compounds exhibited superior binding affinity when compared to Indomethacin (-8.1 kcal/mol). Among the two compounds with the highest binding affinity, 7-O-Methylwogonin was projected to possess the most favorable drug-like properties. Based on this study, it is suggested that further exploration of 7-O-Methylwogonin's potential against inflammation should be pursued using advanced computational methods and in vitro experiments.