Aim: The aim of the study was to evaluate the effectiveness of pretreatment with 5.25% sodium hypochlorite (NaOCl) and ozone gas from microleakage on pit and fissure sealants in primary molars. Materials and methods: A total of 36 noncarious primary molars were decoronated at the cementoenamel junction. These crowns were divided into three groups—NaOCl (n = 12), ozone (n = 12), and control (n = 12). Pretreatment of pits and fissures was done with 5.25% NaOCl for 60 seconds, ozone gas at 100 ppm for 30 seconds, and no pretreatment in the control group. Then, etching, bonding, and sealant application were done. Later, these crowns were subjected to thermocycling. A dye penetration test was done to assess the extent of microleakage using a stereomicroscope. Statistical analysis was done using the Kruskal–Wallis test in G*Power software. Results: The mean microleakage score in the NaOCl group was 2.58, ozone 2.67, and control was 2.75. Comparison between groups showed no significant difference (p = 0888). Conclusion: Pretreatment with ozone gas at 100 ppm and 5.25% sodium showed no statistically significant reduction in microleakage compared to the control group. Clinical significance: Pretreatment of enamel or dentine before sealant placement is hypothesized to remove the hybrid layer, which decreases microleakage and improves the intraoral longevity of sealants. Various mechanical and chemical methods have been used and showed certain promising outcomes. However, in the present study, a comparison of newer material ozone gas against conventional material NaOCl showed no demonstratable reduction in microleakage in primary molars.