Currently, there is only one English-language academic journal dedicated to anime/manga research and criticism:

Mechademia: An Annual Forum for Anime, Manga and the Fan Arts.

However, a paper dealing with anime, manga, the Japanese popular culture industry, or anime/manga fandom can appear in almost any journal that covers some aspect of the humanities and the social sciences. In fact, relevant articles have been also been published in law reviews, medical journals and business-oriented magazines, among others. Nonetheless, several journals have specifically welcomed discussions of Japanese popular culture and its reception worldwide by consistently featuring single articles on anime and manga, organizing theme issues, or issuing calls for papers discussing aspects of Japanese comics and animation, the worldwide anime/manga industry, and the global anime and manga fandom.

These journals include:

/Animation
+ Animation Journal
+ Animation Practice, Process & Production
+ Animation Studies
+ Animation: An Interdisciplinary Journal
+ Animatrix: A Journal of the UCLA Animation Workshop
+ ASIFA Magazine: The International Animation Journal

/Comics
+ Image [&] Narrative
+ ImageTexT: Interdisciplinary Comics Studies
+ International Journal of Comic Art
+ Journal of Graphic Novels and Comics
+ SIGNs: Studies in Graphic Narratives
+ Studies in Comics
+ The Comics Journal

/Film Studies
+ Cinephile: The University of British Columbia's Film Journal
+ Journal of Japanese & Korean Cinema
+ Journal of Religion and Film
+ Post Script: Essays in Film and the Humanities
+ Scope: An Online Journal of Film Studies

/Japanese and East Asian Studies
+ Electronic Journal of Contemporary Japanese Studies
+ Japanese Studies
+ The Journal of Japanese Studies
+ Intersections: Gender, History & Culture in the Asian Context
+ Positions: East Asia Cultures Critique

/Popular Culture
+ Intensities: The Journal of Cult Media
+ Journal of Religion and Popular Culture
+ M/C Journal: A Journal of Media and Culture
+ Refractory: A Journal of Entertainment Media
+ The Journal of Fandom Studies (forthcoming, 2012)
+ The Journal of Popular Culture
+ Transformative Works and Cultures

/Science Fiction
+ Foundation: The International Review of Science Fiction
+ Science Fiction Film and Television
+ Science Fiction Studies