BACKGROUND: Traditionally, treating dental caries involves using rotary instruments, which can create noise that may frighten and cause discomfort in children. Recent research into caries management has introduced minimal invasive techniques like the Papacarie, which is a chemomechanical caries removal agent. OBJECTIVES: To determine and compare the average time taken for caries removal and pain perception during caries removal by Papacarie as a chemomechanical caries removal method with the use of mechanical method using rotary instrument on carious primary molars. METHODOLOGY: This randomized controlled clinical study carried out at the dental clinic in Lagos university teaching hospital. A split-mouth design was used and it involved 50 primary molars in 25 healthy children aged 5-9 years, each child having at least two primary molar teeth with occlusal dentine caries. Each tooth was allocated to the intervention using simple balloting method and treated with either Papacarie or conventional method for caries removal. Outcome measured were caries removal time, pain during caries removal and preference. Pain assessment was blinded. The statistical package for social sciences (SPSS) version 25.0 IBM was used for data analysis. The significance level was set at p ≤ 0.05 for all statistical tests at 95% confidence interval. RESULT: Twenty-five children (with 50 primary molars) met the inclusion criteria and were recruited for the study. The children were between ages 5-9 years. Twenty-five primary molars were treated using Papacarie caries removal method while 25 primary molars were treated using conventional rotary method. There was no statistically significant difference in the time of caries removal between the two groups. Pain perception was lower with the Papacarie method compared to the conventional method, which was statistically significant. More participants preferred the Papacarie method. Twenty-five children (with 50 primary molars) met the inclusion criteria and were recruited for the study. The children were between ages 5-9 years. Twenty-five primary molars were treated using Papacarie caries removal method while 25 primary molars were treated using conventional rotary method. There was no statistically significant difference in the time of caries removal between the two groups. Pain perception was lower with the Papacarie method compared to the conventional method, which was statistically significant. More participants preferred the Papacarie method. CONCLUSION: The findings from this study indicates that the Papacarie demonstrated a comparable caries removal time, lesser pain perception and better acceptability compared to the conventional method of caries removal. TRIAL REGISTRATION: Pan African Clinical Trial Registry (PACTR) Trial number PACTR202111738486539. Registered 18th November 2021.