Abstract Journal impact factors continue to play an important role in research output assessment, in spite of the criticisms and debates around them. The impact factor rankings provided in the Journal Citation Reports (JCR™) database by Thompson Reuters have enjoyed a position of monopoly for many years. But this has recently changed with the availability of the Scopus™ database and its associated journal ranking published in the Scimago Journal Rank (SJR) Web page, as the former provides a citation database with similar inclusion criteria to those used in the JCR and the latter and openly accessible impact factor-based ranking. The availability of alternatives to the JCR impact factor listings using a different citation database raises the question of the extent to which the two rankings can be considered equally valid for research evaluation purposes. This paper reports the results of a contrast of both listings in Computer Science-related topics. It attempts to answer the validity question by comparing the impact factors of journals ranked in both listings and their relative position. The results show that impact factors for journals included in both rankings are strongly correlated, with SJR impact factors in general slightly higher, confirming previous studies related to other disciplines. Nonetheless, the consideration of tercile and quartile position of journal yields some divergences for journals appearing in both rankings that need to be accounted for in research evaluation procedures.