Over the past few decades, there has been an increase in the number of open access (OA) journals in almost all disciplines. This increase in OA journals was accompanied an increase in funding to support such movements. Medical fields are among the highest funded fields, which further promoted its journals to move toward OA publishing. Here, we aim to compare OA and non-OA journals in terms of citation metrics and other indices. We collected data on the included journals from Scopus Source List on 1 November 2018.  We filtered the list for medical journals only. For each journal, we extracted data regarding citation metrics, scholarly output, and wither the journal is OA or non-OA. On the 2017 Scopus list of journals, there was 5835 medical journals. Upon analyzing the difference between medical OA and non-OA journals, we found that OA journals had a significantly higher CiteScore (p< 0.001), percent cited (p< 0.001), and source normalized impact per paper (SNIP) (p< 0.001), whereas non-OA journals had higher scholarly output (p< 0.001). Among the five largest journal publishers, Springer Nature published the highest frequency of OA articles (31.5%), while Wiley-Blackwell had the lowest frequency among its medical journals (4.4%). Among medical journals, although non-OA journals still have higher output in terms of articles per year, OA journals have higher citation metrics.