Selenopyrimidine compounds, though less explored than their thieno[2,3-d]pyrimidine counterparts, exhibit significant potential as multifunctional agents. In this study, a series of novel pyrimidoselenolo[2,3-d]pyrimidine compounds was synthesized using a straightforward methodology. The structural characterization of the compounds was performed using elemental analyses, FT-IR, ¹H NMR, and ¹³C NMR spectroscopy. Their antimicrobial activities were evaluated using the agar well diffusion method against various fungal and bacterial strains, with minimum inhibitory concentrations (MICs) compared to ciprofloxacin and ketoconazole as standards. Compounds with phenyl substituents displayed superior antibacterial and antifungal activities, while amino carboxamide derivatives showed comparatively lower efficacy. Additionally, the luminescence of selected molecules was explored in DMSO solutions and the solid state. Compounds exhibited strong absorption up to 450 nm and concentration-dependent emission behavior, with a clear red shift in emission spectra owing to the molecular aggregation. DFT calculations revealed significant changes in the structure of the ground and excited states, providing insights into the observed luminescence behavior. Molecular docking studies revealed a high affinity of target compounds to topoisomerase II enzyme. All target compounds were predicted to have acceptable physicochemical and pharmacokinetic parameters. Our findings feature the dual potential of selenopyrimidine derivatives as effective antimicrobial agents and promising candidates for luminescent applications. Thanks to combining biocompatibility and emission properties to present these compounds as possible candidates for biological applications such as bioimaging and bioprobes.