 In 1955, Baumgartner founded St. Jude Thaddeus Junior High School, a K-10 school staffed by six Franciscan Sisters of Perpetual Adoration from La Crosse, Wisconsin.Later, the ninth and tenth grades were eliminated, and in the 1980s, the school merged with Cathedral Grade School to form the new Bishop Baumgartner Memorial Catholic School, named in honor of the bishop who founded both of the merging schools.On 14 October 1965, the Vicariate Apostolic of Guam was raised and renamed the Diocese of Agaña, and Apollinaris Baumgartner was appointed its first bishop.