The Jesuit community founded Muffles College in 1953. The school was named for Fr. Joseph Mueffels, a Jesuit resident in Orange Walk at the turn of the 1900. He is noted for having overseen the completion of La Inmaculada Church.
Fr. John Knopp, Superior of the then British Honduras Catholic Mission, was instrumental in the establishment of Muffles. Orange Walk was chosen as the first site for a Jesuit College outside Belize City because the majority of the young men from the districts sitting the entrance examinations for
St. John's College were from Orange Walk.
Assigned to establish the College, Fr. Francis Ring together with Mr Eugene Hernandez, a St. John's graduate originally from Stann Creek and the first Teacher-in-Charge, welcomed twenty-one young men to the new school that first June day. By the next year, increased enrolment necessitated the addition of a new staff member, Orange Walk's own new SJC graduate Uvaldemir Torres, Sr., who was to succeed Mr. Hernandez as administrator in July 1955.
Initially, classes were held in the bottom floor of the presbytery located on Church Street at the time, a few weeks later, however, the students were moved to a fairly large house across the street, rented from Mrs Balbina Gonzalez. The College remained in this location until 1958 when it was relocated across the street from the Parish Church. The street later took the name Muffles Street as a result of this.
In 1957, Muffles College which had begun as a two year institution for young men, went co-ed. Eight young women joined the fourteen young men who now constituted first and second forms. In 1960, Muffles expanded its curriculum to include all four high school years. No longer did the students have to complete their course of studies in Belize City.
When Mr. Belizario Carballo, Sr., one of Muffles' original students, succeeded Mr Torres as administrator in May 1964, the school population had grown to include twenty-four young women and sixty young men.
In 1967, the Sisters of Mercy assumed sponsorship of Muffles College. The first Mercy Principal, Sister Mary Lois Harten, began the development of the current campus, erecting the original three buildings and supervising the move from Muffles Street to Otro Benque in October of that first year. Sister Mary Lois was succeeded by Sister Leona Marie Panton in 1970 who served in this capacity until 1977 when the position was again held by Mr Carballo. He was succeeded by Mr. Frank Garbutt who served until 2004. Mr. Bernaldino Pech served from 2004-2008. The current principal and since 2008 is Mrs. Maria Johnston; she holds a Master’s Degree in Educational Leadership and has served Muffles for the past eighteen years.
In 1992 Muffles College again expanded its services – this time to include a Junior College division. Originally the first Assistant Dean, Mr. Adrian Leiva presently holds the position of Dean of the Junior College.
The College operates under a Board of Governors, which is responsible for the management of its business and academic affairs in accordance with the mission of the Sisters of Mercy