The book was nominated for the 1994 National Book Critics Circle Award.
The Port Washington School District in Port Washington, NY banned this book because it has a detailed diagram depicting how to construct a bomb. "We believe that the purpose of education is to expose students to all areas of reality so that we can make our own judgments. Isn't that why we are able to read Romeo and Juliet without committing suicide, or The Lord of the Flies without being violent? We should not ban a powerful piece of literature just because of a diagram." stated a New York Times opinion piece written by two Schreiber High School students where the book was banned. 
In the Time of the Butterflies is a selection of The Big Read, the National Endowment for the Arts' community-wide reading program, and of "Readers Round Table"(Algonquin).