On 20 July 1980, Vargas y Aruquipa was ordained to the priesthood in the Roman Catholic Diocese of Coroico.[1] He was appointed as an auxiliary bishop of Coroico and as a titular bishop of Bita on 15 Januaury 1992 by Pope John Paul II and was ordained as a bishop at Saint Maria Magdalena Catholic Church in Sorata on 25 March 1992.[1] He was appointed as the Diocesan Bishop of Coroico on 20 August 1997 and served as bishop until his retirement in 2022.[1]
Following a period of political turmoil and protests that led to the resignation of President Gonzalo Sánchez de Lozada on 17 October 2003, Vargas y Aruquipa spoke out about rampant poverty and social and political injustices in Bolivia.[2]