Aim: The aim of this systematic review and meta-analysis was to investigate the possible association between smoking habits and the occurrence of root-filled teeth (RFT) extraction. Material and Methods: The Population, Intervention, Comparison, and Outcome (PICO) question was in adult patients who had RFT, does the absence or presence of smoking habits affect the prevalence of extracted RFT? Systematic MEDLINE/PubMed, Wiley Online Database, Web of Science, and PRISMA protocol was used to evaluate and present the results. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system was used for certainty in the evidence. The risk of bias was assessed according to Cochrane Collaboration common scheme for bias and ROBINS-I tool. Cumulative meta-analysis was performed with a random effects model. PROSPERO registration code: CRD42020165279. Results: After search strategy, 571 articles were recovered, seven were selected for full-text analysis, and two reported data on inclusion criteria, including 516 RFT, 351 in non-smokers, and 165 in smoker subjects. The meta-analysis provided an odds ratio indicating significant association between smoking and the prevalence of extracted RFT (OR = 3.43, 95% CI = 1.17–10.05, p = 0.02, I² = 64%). The certainty of the literature assessment was low per GRADE. Both studies were considered as moderate risk of bias. Conclusions: Tobacco smoking should be considered a negative prognostic factor for the outcome of root canal treatment, although the quality of the evidence is low. RFT of smoking patients are three times more likely to be extracted. Continuing to smoke after endodontic treatment may increase the risk of treatment failure. However, the overall strength of evidence is low. This must be considered a limitation of the present study and the conclusion should be valued with caution.