Scientific collaboration indicates active teamwork between researchers beyond the simple exchange of material or information. This study is a systematic review of the papers published by Iranian researchers, aiming to provide comprehensive indicators, methodologies, and software used for evaluating scientific collaboration. According to guidelines of the Cochrane Handbook, the national and international databases were used for searching by English and Persian keywords without any time limitations. The retrieved articles were managed using EndNote software. By applying the inclusion and exclusion criteria, 201 articles remained for this review. These articles were selected from 93 domestic and foreign journals between 2000 and 2019. The studies used 16 software to extract and analyze scientific collaboration indicators. Systematic review shows that bibliometric and network analysis methods were the main approaches used in scientific collaboration studies among papers published by Iranian researchers (93.5%). More than 25 indicators were extracted from these studies, and they were categorized into patterns of collaboration and co-authorship network analysis. Researchers have revealed an increasing interest in the factors affecting scientific collaboration in recent years. The present study provides comprehensive information on the articles published by Iranian researchers on scientific collaboration. The methodologies and software were identified that are most often used to evaluate scientific collaboration and adapted to direct future research. Still, a variety of indicators situates them in heterogeneous methods of research. This analytical perspective does not locate the evaluation of scientific collaboration at a single spot. Future scientific collaboration studies will continue to evolve to offer more powerful indicators for assessing the knowledge flow status quo.https://dorl.net/dor/20.1001.1.20088302.2022.20.2.13.8