The Raychaudhuri equation for a geodesic congruence in the presence of a zero-point length has been investigated. This is directly related to the small-scale structure of spacetime and possibly captures some quantum gravity effects. The existence of such a minimum distance between spacetime events modifies the associated metric structure and hence the expansion as well as its rate of change deviates from standard expectations. This holds true for any kind of geodesic congruences, including time-like and null geodesics. Interestingly, this construction works with generic spacetime geometry without any need of invoking any particular symmetry. In particular, inclusion of a zero-point length results into a non-vanishing cross-sectional area for the geodesic congruences even in the coincidence limit, thus avoiding formation of caustics. This will have implications for both time-like and null geodesic congruences, which may lead to avoidance of singularity formation in the quantum spacetime.