We study instanton corrections to four-point correlation correlation function of half-BPS operators in $mathcal N=4$ SYM in the light-cone limit when operators become null separated in a sequential manner. We exploit the relation between the correlation function in this limit and light-like rectangular Wilson loop to determine the leading instanton contribution to the former from the semiclassical result for the latter. We verify that the light-like rectangular Wilson loop satisfies anomalous conformal Ward identities nonperturbatively, in the presence of instantons. We then use these identities to compute the leading instanton contribution to the light-like cusp anomalous dimension and to anomalous dimension of twist-two operators with large spin.