Background Outcomes of patients with autoimmune diseases after percutaneous coronary intervention (PCI), as compared to those without autoimmune disease, remain unclear. Methods We searched Medline, EMBASE, and the Cochrane Library from their inception to 1 April 2017. All studies comparing the following outcomes of patients with and without autoimmune diseases after PCI were included: long-term mortality, major adverse cardiovascular events (MACE), repeat revascularisation, myocardial ischaemia or myocardial infarction (MI), restenosis, and in-hospital mortality. The Newcastle-Ottawa Quality Assessment Scale (NOS) and the quality assessment form of the Agency for Healthcare Research and Quality (USA) (AHRQ) were used for assessing the risk of bias, and the certainty of evidence was rated by the Grading of Recommendations Assessment, Development, and Evaluation (GRADE). Results A total of 11 studies were included in our analysis. Compared with patients without autoimmune diseases, those with autoimmune diseases carried an increased risk of MACEs (relative risk (RR): 2.24, 95% confidence interval (CI): 1.20-4.16; heterogeneity: p = 0.128, I-2 = 56.9%), repeat revascularisation (RR: 1.66, 95% CI 95%: 1.01-2.72; heterogeneity: p = 0.057, I-2 = 65.1%), ischaemia or MI (RR: 2.80, 95% CI: 1.38-5.65; heterogeneity: p = 0.871, I-2 = 0.0%), and restenosis (RR: 2.06, 95% CI: 1.39-3.07; heterogeneity: p = 0.665, I-2 = 0.0%) during the one-year follow-up after PCI, and carried an increased risk of MACEs (RR: 1.10, 95% CI: 1.04-1.17) and death (RR 1.38, 95% CI: 1.25-1.51) during the 11-year follow-up after PCI. Conclusions Evidence of very low quality showed that during the one-year follow-up period, patients with autoimmune diseases after PCI were more likely to experience MACEs, repeat revascularisation, myocardial ischaemia or ML and restenosis. During the 11-year follow-up period, patients with autoimmune diseases after PO were more likely to die. It is therefore important to watch for restenosis, repeat ischaemia or MI and other adverse events more carefully in patients with autoimmune diseases after PCI.