Herein, we describe a surfactant‐catalyzed green methodology for electrophilic substitution reaction of 6‐aminouracil derivatives with various aldehydes that were neither reported earlier nor produced using conventional routes. Optimized results show the importance of anionic surfactant (SDS) on the reaction between hydrophilic and hydrophobic compounds in aqueous medium. All synthesized compounds were characterized by various spectroscopic methods like FTIR, NMR, HRMS, and SC‐XRD. Furthermore, the surfactant remediation from the reaction mixture was done using graphene oxide (GO). The results from batch‐adsorption studies indicate prominent sorption of SDS onto the surface of GO with an adsorption efficiency of ~84.9 %. The SDS adsorbed onto GO were analyzed using UV‐vis, FT‐IR, Raman, and HRTEM analysis. Next, the synthesized compounds were screened for their potential anti‐SARS‐CoV2 activity due to their structural resemblance with pyrimidine analogs acting as anti‐viral agents. The in‐silico results indicate that the synthesized compounds exhibit the highest inhibitory activity towards RdRp with binding energy −9.55 kcal/mol. In contrast, Remdesivir showed only −6.45 kcal/mol. In addition, upon preliminary screening of the compounds for possible antimicrobial activity (antifungal and anti‐leishmanial), 4 bf showed moderately high inhibitory activity with IC50 values of 205.48 μM and 124.97 μM for fungal and leishmanial strains, respectively.