In June 1967, just two years after its opening, Father Fahey was appointed librarian at Pope St. John XXIII National Seminary. He briefly lived in residence at St. Linus Rectory in nearby Natick and after moving to residence in seminary, he continued to assist in the Natick parish in weekends.

In the years at Weston, he served not only the students and faculty but also with seven of the seminary's eight rectors. In 1996 he returned to parish ministry, serving briefly as a parochial vicar at St. Patrick Parish, Natick.

Cardinal Bernard Law appointed him pastor to St. Margaret Parish in Beverly on July 1, 1997. The small parish nestled amidst the often towering and expansive manses of the Beverly Farms area was a good fit for both the new pastor and the parish.

In 2009, Father Fahey resigned as pastor in Beverly, having celebrated his golden jubilee of priestly ordination earlier that year. During his retirement he lived for some years in residence at St. Mary Rectory in Georgetown, where he also assisted the pastor with regular parish duties.

Father Fahey died on March 16 at Marian Manor, South Boston where he had been under the care of the Carmelite Sisters of the Aged and Infirm for some months.

His funeral Mass was celebrated on March 21 at St. Mary Church, Georgetown. Merrimack Regional Bishop Robert Hennessey was the principal celebrant of the Mass; former rector of Pope St. John Seminary, Msgr. Cornelius McRae, now of St. John's Seminary, was the homilist and concelebrating were Father Richard Burton, present pastor of St. Mary, Georgetown and the parish's previous pastor, Father Robert Poitras, administrator of Our Lady of Grace Parish, Pepperell. Following the funeral Mass, Father Fahey was buried in St. Joseph Cemetery, West Roxbury.