Cracks in concrete that could decrease the concrete element's life span need to be repaired. The autogenous healing mechanism, a feature provided by cementitious material due to continuous hydration and calcium carbonate precipitation, could be a solution to mitigate cracks in concrete elements. In this research, alkali-activated lightweight aggregate produced from fly ash (FA LWA) that could retain water in their pores to induce further hydration at a later age could become a promising material to provoke an autogenous healing mechanism. The mortar was mixed with FA LWA and expanded clay LWA (EC LWA) at a replacement rate of 30% by volume for fine aggregate. The outcomes demonstrate that the flowability of the fresh mortar was not considerably impacted by the addition of LWA. The compressive strength of mortar incorporating FA LWA was comparable to the mortar that contains EC LWA. The healing ratio of the reference sample, the sample incorporating FA LWA and EC LWA in the crack with the width range of 0.3–0.4 mm, was 33, 95, and 53%, respectively. In conclusion, FA LWA could successfully provoke the autogenous healing mechanism in mortar.