La Fountain-Stokes was born and raised in San Juan, Puerto Rico, specifically in Miramar, a traditional neighborhood located in the central district of Santurce. He was adopted at birth by Donald and Ramona La Fountain, and is the brother of the ESPN newscaster Michele La Fountain. He has written about his childhood experiences in an essay called "Los nenes con los nenes y las nenas con las nenas" [Girls with Girls, and Boys with Boys], where he describes his childhood home as bilingual and bicultural. His essay "Queer Diasporas, Boricua Lives: A Meditation on Sexile" also discusses some of these early experiences.

La Fountain-Stokes received all of his primary and secondary education at the Academia del Perpetuo Socorro, an elite bilingual school run by the School Sisters of Notre Dame. He graduated from high school in 1986. He then studied at Harvard College in Cambridge, Massachusetts, where he received his Bachelor of Arts degree in Hispanic Studies in 1991. While in college, La Fountain-Stokes spent a year and a half studying at the University of São Paulo in Brazil. He later went on to obtain a Master’s degree and Doctorate in Spanish from Columbia University in New York City.

La Fountain-Stokes started his teaching career as an assistant professor at the Ohio State University (1998—1999) and then taught at Rutgers, The State University of New Jersey for four years (1999—2003). Since 2003, he has taught Latino studies, American studies, and Spanish at the University of Michigan, including courses on queer Hispanic Caribbean culture, LGBT studies and Latino literature, theater, performance, and film. He was promoted to associate professor with tenure in 2009. His interviews in Spanish with leading Latino artists, journalists, and scholars such as the Uruguayan novelist and pop singer Dani Umpi and the Los Angeles Times journalist Sam Quiñones appear on the "University of Michigan in Spanish" channel on YouTube and on iTunes U.

La Fountain-Stokes's academic writing has focused mostly on queer Puerto Rican culture. His book Queer Ricans: Cultures and Sexualities in the Diaspora (University of Minnesota Press, 2009) discusses LGBT Puerto Rican migration from a cultural studies perspective, with chapters on Luis Rafael Sánchez, Manuel Ramos Otero, Luz María Umpierre, Frances Negrón-Muntaner, Rose Troche, Erika Lopez, Arthur Aviles, and Elizabeth Marrero. Queer Ricans is based on La Fountain-Stokes's Ph.D. dissertation, which he wrote under the supervision of Jean Franco. The author received funding for this project in 1997 from the International Migration Program at the Social Science Research Council.

He is currently working on a new book titled Translocas and Transmachas: Trans Diasporic Puerto Rican Drag which is on Puerto Rican and diasporic theater, performance, and activism since the 1960s, and on the links between cross-dressing, sex/gender modification, and physical displacement in a geographic zone marked by frequent migrations. In this project, La Fountain-Stokes analyzes the work of a number of contemporary performers and activists including Sylvia Rivera, Holly Woodlawn, Mario Montez, Freddie Mercado, Jorge Merced, Eduardo Alegría, Javier Cardona, Lady Catiria, Elizabeth Marrero, and Erika Lopez. He has another less developed book project on the use of animal words such as pato (duck in Spanish) to refer to homosexuality in Puerto Rico and the Caribbean.

La Fountain-Stokes has published scholarly articles in journals such as CENTRO Journal, Revista Iberoamericana, and A Journal of Lesbian and Gay Studies, including his essay on his travels to Cuba, "De un pájaro las dos alas," which first appeared in GLQ in 2002 and was reprinted in Our Caribbean: A Gathering of Lesbian and Gay Writing from the Caribbean, edited by the Jamaican American gay writer Thomas Glave. La Fountain-Stokes describes this article as a "fictionalized, experimental narrative or autoethnography based on [his] travel experiences as a gay Puerto Rican theater critic and former graduate student."

La Fountain-Stokes frequently publishes short newspaper articles in Spanish, particularly in En Rojo, the cultural supplement of the Puerto Rican weekly Claridad. These include theater and performance reviews, book reviews, and essays on popular culture, such as his piece on a calendar by the popular Puerto Rican male model and former police officer Peter Hance. La Fountain-Stokes is also a frequent speaker at professional meetings and college campuses, and has talked about his work in several countries, including Brazil, Cuba, Mexico, Venezuela, and Spain. He has also been actively involved in a number of professional organizations, particularly the Modern Language Association, the Latin American Studies Association, the Puerto Rican Studies Association, the Caribbean Studies Association, and the City University of New York Center for Lesbian and Gay Studies (CLAGS), holding positions of leadership in several of these.

La Fountain-Stokes is best known as an author of short stories, but he has also published poetry and received awards for his plays. He has also done some performing, specifically his 2004 one-man show Abolición del pato/Abolition of the Duck, which he did as part of the Casa Cruz de la Luna First Experimental Festival in San Germán, Puerto Rico, and later at the Bronx Academy of Arts and Dance Out Like That Festival. The Village Voice described Abolition of the Duck as "This is not Avenue Q" in reference to the artist's use of indigenous dolls as puppets to talk about Puerto Rican homosexuality.

La Fountain-Stokes' short stories have appeared in a number of anthologies such as Bésame Mucho: New Gay Latino Fiction (1999) and Los otros cuerpos: Antología de temática gay, lésbica y queer desde Puerto Rico y su diáspora (2007). He has also published in journals and websites such as Blithe House Quarterly and Harrington Gay Men’s Fiction Quarterly. His first book of short stories is called Uñas pintadas de azul/Blue Fingernails (Bilingual Press/Editorial Bilingüe, 2009) and includes 14 short stories written in the 1990s and early 2000s, some of them while the author was enrolled in a creative writing workshop taught by the Chilean author Diamela Eltit.

Most of La Fountain-Stokes's stories focus on gay Puerto Rican characters, and sometimes incorporate elements of science fiction and fantasy. The scholar Enrique Morales-Díaz has written extensively about one of these stories, "My Name, Multitudinous Mass," describing La Fountain-Stokes as a "Diasporican" author.

La Fountain-Stokes's plays include ¡Escándalo! (2003) and Uñas pintadas de azul (2006, an extension of a short story included in his book of short stories). Both of these plays have been read publicly as part of the Pregones Theater Asunción Playwrights Project in the Bronx, but neither one has been staged.