We performed a meta-analysis to compare therapeutic outcome/safety of drug-eluting stent (DES) and conventional in-stent restenosis (ISR) treatments. We browsed through large volume of clinical data by searching MEDLINE, EMBASE, Cochrane central register of controlled trials, and EBSCO databases. In this study, 11 randomized controlled trials, 17 non-randomized controlled trials, 6,330 patients, and 6,662 lesions were included. Clinical and coronary angiography follow-up for 6-16 months was included. The major outcomes were target lesion revascularization (TLR) and major adverse cardiac events (MACE). We found that DES showed advantage in TLR (OR = 0.46; 95 % CI: 0.34, 0.62; P < 0.00001), MACE (OR = 0.51; 95 % CI: 0.34, 0.77; P = 0.001), Late Lumen Loss (IV = -0.30; 95 % CI: -0.44, -0.15; P < 0.0001), stenosis of lumen diameter (OR = -17.45; 95 % CI: -23.69, -11.21; P < 0.00001), and restenosis (OR = 0.26; 95 % CI: 0.17, 0.40; P < 0.00001) over conventional ISR treatment. Regarding cardiac death (OR = 0.80; 95 % CI: 0.55, 1.17; P = 0.25), myocardial infarction (OR = 1.00;95 %CI: 0.66, 1.51; P = 1.00) and late thrombosis (OR = 0.70; 95 % CI: 0.42, 1.17; P = 0.18), there was no significant difference between different treatments. We, therefore, concluded that in treating percutaneous coronary intervention-ISR, DES was more effective in reducing incidence of TLR, MACE, and restenosis, and decreasing severity of late lumen loss/stenosis of lumen diameter compared with bare metal stent, percutaneous transluminal coronary angioplasty, intracoronary brachytherapy, and cutting balloon treatments. There was no significant difference between DES and conventional therapy for ISR. As suggested by current statistical analysis, DES after ISR did not involve a higher incidence of cardiac death, myocardial infarction, and thrombosis.