This review article aims to use a meta-analytical approach to systematize and compare the main effects of green and red propolis, as determined through biological assays, in order to inform future preclinical tests and drug development for this natural product. A search for the full spectrum of their biological properties and possible pharmacological and medical applications found that propolis has anti-inflammatory, antioxidant, antiviral, antibacterial, antifungal, antiparasitic, antiproliferative, anticarcinogenic, antinociceptive and neuroprotective effects, arising mainly from polyphenolic compounds. In order to identify and retrieve the most important published literature in this field in the last ten years a database search (LILACS, PubMed, Scopus and Web of Science) was performed. The MeSH terms and free text words used were: green propolis, red propolis, anti-inflammatory, antioxidant, antimicrobial, antiviral, antibacterial, antifungal, antiparasitic, anticarcinogenic, antiproliferative, cytotoxicity, analgesic, antinociceptive, neuroprotective and neuroregenerative as well as their respective combinations. The meta-analysis outcomes showed that red propolis is superior to green propolis for healing, cytotoxic, antiparasitic and antibacterial applications; however, there are no significant differences between them as regards antifungal, antioxidant and anti-inflammatory activities. Furthermore, it was found that red propolis contains greater amounts of flavonoids than green propolis, and that the supercritical extraction method was better in relation to phenolic acid yields, whereas the ethanolic method was better in respect of flavonoids. The key findings of this study can help to direct future work on this natural product in the pharmacological and medical fields.