Objective To clarify the prognosis and prognostic factors of interstitial pneumonia with autoimmune features (IPAF) in comparison to idiopathic pulmonary fibrosis (IPF), the most common idiopathic interstitial pneumonia, and connective tissue disease-associated interstitial pneumonia (CTD-IP). Design A systematic review and meta-analysis. Data sources Electronic databases such as Medline and Embase were searched from 2015 through 6 September 2019. Eligibility criteria for selecting studies Primary studies that comparatively investigated the prognosis or prognostic factors of IPAF were eligible. Data extraction and analysis Two reviewers extracted relevant data and assessed the risk of bias independently. A meta-analysis was conducted using a random-effects model. The quality of presented evidence was assessed by the Grades of Recommendation, Assessment, Development, and Evaluation system. Results Out of a total of 656 records retrieved, 12 studies were reviewed. The clinical features of IPAF were diverse between studies, which included a radiological and/or pathological usual interstitial pneumonia (UIP) pattern of between 0% and 73.8%. All studies contained some risk of bias. There was no significant difference of all-cause mortality between IPAF-UIP and IPF in all studies, although the prognosis of IPAF in contrast to IPF or CTD-IP varied between studies depending on the proportion of UIP pattern. Among the potential prognostic factors identified, age was significantly associated with all-cause mortality of IPAF by a pooled analysis of univariate results with a hazard ratio (HR) of 1.06 (95% confidence interval (CI) 1.04 to 1.07). The adjusted effect of age was also significant in all studies. The quality of presented evidence was deemed as very low. Conclusion There was no significant difference of all-cause mortality between IPAF-UIP and IPF. Age was deemed as a prognostic factor for all-cause mortality of IPAF. The findings should be interpreted cautiously due to the low quality of the presented evidence. PROSPERO registration number CRD42018115870.