Proton-proton ($pp$) collision has been considered as a baseline to study the system produced in relativistic heavy-ion (AA) collisions with the basic assumption that no thermal medium is formed in $pp$ collisions. This warrants a cautious analysis of the system produced in $pp$ collisions at relativistic energies.In this work we investigate the charmonium suppression in $pp$ collisions at $sqrt{s} = 7$ and $13$ TeV to inspect the system formed in these collisions. In this work, charmonium suppression has been studied for various event multiplicities and transverse momenta by including the mechanisms of color screening, gluonic dissociation, collisional damping along with the regeneration due to correlated $cbar c$ pairs. Here we obtain a net suppression of charmonia at high-multiplicity events indicating the possibility towards the formation of quark-gluon plasma in $pp$ collisions.