Objective The aim was to compare the cost-effectiveness of partial caries removal (PCR) and stepwise caries removal (SW) in mature permanent teeth diagnosed with deep caries lesions, in a Swedish Public Dental Care organization. Materials and methods A decision tree model was used to calculate the cost-effectiveness for PCR and SW. Probability values were obtained through a literature search in PubMed and Scopus. Treatment times were estimated by a group of dentists practicing at public dental care clinics in Vastra Gotaland county, Sweden. Results The expected costs for PCR and SW were 187,63 and 414,35 euro, respectively, indicating that PCR was more cost-effective. Four articles were identified through the literature search. The p-values for PCR outcomes were 94% (success), 0% (pulp exposure) and 6% (pulpitis/apical periodontitis etc.). For SW, the p-values were 76% (success), 2% (pulp exposure during the first visit), 13% (pulp exposure during the second visit) and 9% (pulpitis/apical periodontitis etc.). Conclusions Given the presumptions in this decision analysis, the PCR method used on mature permanent teeth is more cost-effective (p < ,05) compared to the SW method in protecting the pulp from exposure and avoiding the need for root canal treatment.