Severe pathogen infections, such as Monkeypox disease caused by the Monkeypox virus, easily spread in different animals and then into humans. There is an urge for novel therapeutic options, such as medicine/vaccine development to control it. Therefore, we designed Pinocembrin derivatives and performed in silico analysis such as molecular docking by PyRx software, molecular dynamics (MD) simulations at 100 ns, binding free energy estimation by AMBER20 software, ADMET profile, and Pass prediction. Optimal results were observed for two derivatives (07 and 11), exhibiting interactions with key residues of the selected protein. These interactions were substantiated by a range of structural and energetic parameters, including binding energies, solvation-free energy models, dynamic fluctuations, hydrogen bonding, and solvent accessibility. Notably, ligands 07 and 11 displayed exceptional binding affinities of −10.3 kcal/mol and −9.6 kcal/mol, respectively. RMSD value presented minor abruptions of about 1.2 to 1.3 Å and superimposed structures of selected derivatives complexes with Monkeypox target protein at 0 ns and 100 ns presented minor fluctuation in the native and bounded conformation. Slight instability is noted from the peaks in graphs of RMSD, RMSF, hydrogen bonds (HBs), beta factor (BF), and solvent-accessible surface area (SASA). Based on promising results, we proposed that Pinocembrin derivatives may serve as novel therapeutic agents against Monkeypox infections. Therefore, strongly advocate for further experimental validation through chemical laboratory testing. Such endeavors could pave the way for the development of effective treatments to mitigate the impact of Monkey-Pox disease.