JMIR is indexed in more than 18 bibliographic databases and abstracting services, including MEDLINE [Index Medicus], PubMed, PMC, Directory of Open Access Journals (DOAJ Seal), CINAHL, Information Science Abstracts, INSPEC (Institution of Electrical Engineers), Communication Abstracts, The Informed Librarian Online, LISA (Library and Information Science Abstracts), EMBASE, Scopus, Science Citation Index Expanded, PsycINFO, CABI, LISTA (Library / Information Sciences & Technology Abstracts), ASSIA (Applied Social Sciences Index and Abstracts) database, CSA Social Services Abstracts database, EBSCO, and others.

In 2024, JMIR received a Journal Impact Factor™ of 5.8 (5-Year Journal Impact Factor™: 6.7) according to the latest release of the Journal Citation Reports™ from Clarivate, 2024.

JMIR continues to be a Q1 journal in many categories and many indices, for example:

* Q1 journal in "Health Informatics" (Scopus data: CiteScore 14.4, ranked 7/138, 95th percentile)
* Q1 journal in "Health Care Sciences & Services" (ranked 9/174) (Source: Journal Citation Reports™ from Clarivate, 2023)
* Q1 journal in "Medical Informatics" (ranked 5/44) (Source: Journal Citation Reports™ from Clarivate, 2023)
* Q1 journal by Scimago Journal Rank (Health Informatics)
* Q1 journal ranked #1 on Google Scholar "Medical Informatics"

In the German VHB Ranking of Business journals, J Med Internet Res has a B-rating, corresponding to "important and reputable journals" ("wichtige und angesehene wissenschaftliche Zeitschriften").