Dr. Edmund D. Pellegrino, president of the Yale-New Haven Medical Center, was named the 12th president of the Catholic University yesterday.

Pellegrino, 58, a physician who also is a professor of medicine at the Yale Medical School, succeeds Clarence C. Walton, who is returning to teaching at Columbia University after almost 10 years as president of Catholic Unversity.

The second lay president of Catholic University, Pellegrino has served as vice president for health sciences at the State University of New York. Stony Brook and at the University of Tennessee, Pellegrino also is one of the few physicians serving as a college or university president in this country.

In addition to his work as an administrator, Pellegrino has published a number of papers dealing with questions of medicine and moral, ethical and philosophical concern.

In 1971 Pellegrino was offered, and turned down, the post of assistant secretary for health of the Department of Health, Education and Welfare. Pellegrino said at the time that he could not accept the position because he was needed at Stony Brook.

Pellegrino's appointment is effective Sept. 1.

Catholic, which has about 5,000 graduate and 2,500 undergraduate students, was founded in 1889. It is the only university in the United States, and one of only three outside Rome, that is empowered to grant pontifical degrees.

Catholic University is the national university of the Catholic Church in the United States. It has nine schools - arts and sciences, education, engineering and architecture, law, music, nursing, philosophy and social service and the school of religious studies.

Walton, who taught business and economics at Columbia University's School of Business and served as the dean of Columbia's School of General Studies prior to coming to Catholic University in 1969, was the first lay president in the school's 89-year history.

According to Archbishop Philip M. Hannan of New Orleans, chairman of the university's board of trustees, more than 100 candidates were considered for the presidency prior to Pellegrino's selection.

Pellegrino, in a brief statement accepting the appointment, said, "I welcome the opportunity to employ my academic experiences and particularly my concerns for the future of both the humanities and the sciences in the service of Catholic higher education."

University officials declined to say what Pellegrino's salary as president would be.