There have been quite a few in our history:
 
Mary Gnaedinger, Famous Fantastic Mysteries, 1939-1953 / A. Merritt's Fantasy Magazine, 1949-1950.
Dorothy McIlwraith, Weird Tales, 1940-1954.
Beatrice Mahaffrey, Imagination, 1950; Universe Science Fiction, 1953-1955.
Lila E. Shaffer. Amazing Stories, 1951-1953.
Beatrice Jones, Fantastic Universe, 1954; assisted on Other Worlds, 1950-1955.

Cele Goldsmith, Amazing Stories / Fantastic Stories, 1959-1965.
Judy-Lynn Del Rey, Galaxy, 1969-1973, If, 1969-1973, Worlds of Tomorrow, 1970-1971, Worlds of Fantasy, 1970-1971.
Sharon Moore, Science Fiction Yearbook, 1970
Anne Keffer, Science Fiction Yearbook, 1971.
Cylvia Kleinman, Weird Tales, 1973-1974.
Hilary Bailey, New Worlds, 1974-1976.
Julie Davis, Science Fiction Monthly, 1974-1976 / SF Digest, 1976.
Bonnie Leigland, Galaxy, 1974 / Worlds of Fantasy, 1974.
Pat Cadigan, Shayol, 1977-1985,
Rose Kaplan, Cosmos, 1977.
Lois Wickstrom, Pandora, 1978-1987, with Jean Lorrah after Issue 10.
Elinor Mavor (as Omar Gohagen), Amazing Stories, 1979-1982 / Fantastic, 1979-1980.
Liz Danforth, Sorcerer's Apprentice, 1980-1983.
Ellen Datlow, Omni, 1981-1998 / Event Horizon, 1998-1999 / SciFiction, 2000-2005.
Kathleen Moloney, Asimov's, 1982.
Shawna McCarthy. Asimov's. 1983-1985 / Realms of Fantasy, 1994-present.
Kristine Kathryn Rusch, Pulphouse, 1988-1993 / F&SF, 1991-1997.
Marion Zimmer Bradley, Marion Zimmer Bradley's Fantasy Magazine, 1988-1999.
Diane Walton, OnSpec, 1989-present.
Barbara Roden, All Hallows, 1994-present.
Kelly Link, Lady Churchill's Rosebud Wristlet, 1996-present.
Mary Anne Mohanraj, Strange Horizons, 2000-2003.
Paula Guran, Horror Garage, 2001-2002.
Eileen Gunn Infinite Matrix, 2001-2008.
Liz Holliday, Odyssey, ? ? 
Mary Anne Mohanraj, Strange Horizons, 2000-2003.
Susan Marie Groppi, Strange Horizons, 2000-present.
Chris Heinemann, Strange Horizons, 2000-2003.
Karen Meisner, Strange Horizons, 2003-present.
Sheila Williams, Asimov's, 2004-present.
Beth Wodzinski. Shimmer Magazine, 2005-present.
Wendy S. Delmater, Abyss & Apex, 2005-present
Sara King, Aberrant Dreams, 2007-present.
Ann VanderMeer, Weird Tales, 2007-present.
Hildy Silverman, Space and Time, 2007-present.
Cat Rambo. Fantasy Magazine. 2008-present.

Any I'm missing? I can't access my research volumes right now, so I apologise!