We compare the network of aggregated journal–journal citation relations provided by the Journal Citation Reports (JCR) 2012 of the Science Citation Index (SCI) and Social Sciences Citation Index (SSCI) with similar data based on Scopus 2012. First, global and overlay maps were developed for the 2 sets separately. Using fuzzy‐string matching and ISSN numbers, we were able to match 10,524 journal names between the 2 sets: 96.4% of the 10,936 journals contained in JCR, or 51.2% of the 20,554 journals covered by Scopus. Network analysis was pursued on the set of journals shared between the 2 databases and the 2 sets of unique journals. Citations among the shared journals are more comprehensively covered in JCR than in Scopus, so the network in JCR is denser and more connected than in Scopus. The ranking of shared journals in terms of indegree (i.e., numbers of citing journals) or total citations is similar in both databases overall (Spearman rank correlation ρ > 0.97), but some individual journals rank very differently. Journals that are unique to Scopus seem to be less important—they are citing shared journals rather than being cited by them—but the humanities are covered better in Scopus than in JCR.