Schrank is a local Bangladeshi plant well-accepted by the tribal population for its medicinal properties. The primary approach of our study was to uncover the analgesic and anti-inflammatory potential of methanol extract of stem in mice model with in silico molecular docking and molecular dynamics simulation approach. Phenolic compounds were identified and quantified from the extract through high-performance liquid chromatography-diode array detector (HPLC-DAD) analysis. Writhing assay through injection of acetic acid, licking assay through formalin injection, and finally, hot plate assay was employed to observe the analgesic activity. The carrageenan-induced paw edema model was employed to determine the anti-inflammatory potential of the extract. In silico molecular docking and molecular dynamics were also run to validate the in vivo study results. Eight polyphenolic compounds from the extract were identified and quantified via HPLC-DAD analysis, and (-) epicatechin was most abundantly distributed (87.15 ± 0.24 mg/100 g dry extract). In vivo study revealed that 400 mg/kg dose significantly inhibited (P < 0.01) the writhing response in the writhing assay and demonstrated the highest percent of inhibition of licking (70.67%) in the late part of the licking test. The same extract dose produced the highest (74.71%) percent of maximal effect (% MPE) in the hot plate assay. It demonstrated the highest percent of edema inhibition (68.00%) in the fourth hour of the paw edema assay. Molecular docking and molecular dynamics simulation of (-) epicatechin, caffeic acid, and kaempferol with cyclooxygenase-2 revealed that they have similar interactions to the standard inhibitor celecoxib. These valuable bioactive compounds may induce significant analgesic and anti-inflammatory properties in MECCS. Therefore, based on the findings of this study, it can be concluded that stem can be a prospect in the medicinal field due to its remarkable analgesic and anti-inflammatory effect.