Objective To systematically review the effectiveness of different therapies for chronic periapical lesion (CPL), such as different root canal surgeries and conventional root canal obturation. Methods The following databases such as The Cochrane Library, MEDLINE, EMbase, VIP, CNKI, CMB and WanFang Data were searched to collect the randomized controlled trials (RCTs) and concurrent controlled trials (CCTs) on CPL treated by both conventional root canal obturation and different root canal surgeries such as periapical curettage, retrograde obturation and apicoectomy. The references of the included studies were also retrieved, and the retrieval time was from inception to October 2012. Two reviewers independently screened the literature according to the inclusion and exclusion criteria, extracted the data, and assessed the quality. Then after cross-checking, the meta-analyses were performed by using RevMan 5.0 software. Results A total of 7 RCTs and 11 CCTs involving 1 663 patients were included. Among all 1 727 teeth, 1 661 met the inclusion criteria which contained 1 151 in the root canal surgeries groups, and 510 in the conventional groups. The methodological quality of all included studies was low. The results of meta-analysis showed that, in general, different root canal surgeries plus conventional root canal obturation were more effective than root canal obturation alone (RR=1.12, 95%CI 1.08 to 1.18, Plt;0.000 01). The results of sub-group analysis revealed that, the total effective rate of both retrograde obturation (RR=1.3, 95% CI 1.15 to 1.46, Plt;0.000 1) and apicoectomy (RR=1.23, 95% CI 1.04 to 1.46, P=0.02) was superior to that of periapical curettage, with significant differences in both sub-groups. But retrograde obturation took similar effect as apicoectomy did, without a significant difference (RR=0.96, 95% CI 0.83 to 1.11, P=0.61). Conclusion This systematic review suggests that, root canal obturation plus root canal surgeries is superior to root canal obturation alone in treating chronic periapical lesions. The comparison among different root canal surgeries reveals that, both apicoectomy and retrograde obturation are superior to periapical curettage. For the quantity and quality limitation of the included studies, additionally, the possibly existing bias because it is difficult to conduct surgeon and patient blind methods in root canal obturation and root canal surgeries in clinic, so the above conclusion has to be further proved by performing more well-designed and high quality RCTs.