In vortex-like spin arrangements, multiple spins can combine into emergent multipole moments. Such multipole moments have broken space-inversion and time-reversal symmetries, and can therefore exhibit linear magnetoelectric (ME) activity. Three types of such multipole moments are known: toroidal; monopole; and quadrupole moments. So far, however, the ME activity of these multipole moments has only been established experimentally for the toroidal moment. Here we propose a magnetic square cupola cluster, in which four corner-sharing square-coordinated metal-ligand fragments form a noncoplanar buckled structure, as a promising structural unit that carries an ME-active multipole moment. We substantiate this idea by observing clear magnetodielectric signals associated with an antiferroic ME-active magnetic quadrupole order in the real material Ba(TiO)Cu4(PO4)4. The present result serves as a useful guide for exploring and designing new ME-active materials based on vortex-like spin arrangements.