June Wayne's artworks are in the permanent collection of dozens of museums world wide. Here is a partial list of those public collections. Click links to view works in museums showing their collections online.

• Achenbach Foundation for the Graphic Arts, Fine Arts Museums of San Francisco

• Amon Carter Museum, Fort Worth

• Arizona State University Art Museum, Tempe

• Art Institute of Chicago

• Bibliotheque nationale de France, Paris

• Bibliotheque royale de Belgique, Brussels

• Birmingham Museums and Art Gallery, Birmingham, England

• Blanton Museum of Art, University of Texas at Austin

• Block Museum of Art, Northwestern University, Evanston, Illinois

• British Museum, London

• Brodsky Center (formerly Rutgers Center for Innovative Print and Paper), Rutgers University, New Brunswick, New Jersey

• Cincinnati Art Museum

• Columbia Museum of Art, South Carolina

• Des Moines Art Center

• DePauw University Art Center, Greencastle, Indiana

• Free Library of Philadelphia

• Fresno Art Museum

• Grand Rapids Art Museum

• Grunwald Center for the Graphic Arts, Hammer Museum, University of California at Los Angeles

• Houghton Library, Harvard University, Cambridge, Massachusetts

• Jewish Museum, New York

• Jundt Art Museum, Gonzaga University, Spokane

• Krannert Art Museum, University of Illinois at Urbana-Champaign

• Lehigh University Art Galleries, Bethlehem, Pennsylvania

• Library of Congress, Washington, D.C.

• Long Beach Museum of Art

• Los Angeles County Museum of Art

• McNay Art Museum, San Antonio

• Museum of Contemporary Art, San Diego

• Museum of Modern Art, New York

• National Gallery of Art, Washington, D.C.

• National Gallery of Austrailia, Canberra

• National Museum of American History, Smithsonian Institution, Washington, D.C.

• National Museum of Women in the Arts, Washington, D.C.

• National Portrait Gallery, Smithsonian Institution, Washington, D.C.

• Neuberger Museum of Art, Purchase College, State University of New York

• New York Public Library

• Norton Simon Museum, Pasadena

• Oakland Museum of California

• Palm Springs Desert Museum

• Philadelphia Museum of Art

• Pomona College Museum of Art, Claremont, California

• Princeton University Library, New Jersey

• Queensland Art Gallery, Brisbane, Australia

• San Diego Museum of Art

• Santa Barbara Museum of Art

• Skirball Cultural Center, Los Angeles

• Smithsonian American Art Museum, Washington, D.C.

• Sweeney Art Gallery, University of California, Riverside

• Syracuse University Art Collection, New York

• University of Arizona Museum of Art, Tucson

• University of Iowa Museum of Art, Iowa City

• University of New Mexico Art Museum, Albuquerque

• Victoria and Albert Museum, London

• Walker Art Center, Minneapolis

• Weisman Art Museum, University of Minnesota, Minneapolis

• Whitney Museum of American Art, New York

• Williams College Museum of Art,

• Williamstown, Massachusetts

• Zimmerli Art Museum, Rutgers University, New Brunswick, New Jersey