Varela was built as an overcrowding reliever for G. Holmes Braddock High School and Miami Sunset High School; construction began in 1998 but due to several delays in construction (mainly concerning funding and local area politics) the school's opening was pushed back several times. Varela finally opened in the Fall of 2000.
The school was named for Father Félix Varela, a Cuban priest from the 19th century, and a popular figure for Cubans in Miami.
It opened its doors to about 2,000 ninth and tenth graders (classes of 2003 and 2004) on August 28, 2000. Enrollment at Varela High grew sequentially after each school year as more incoming freshmen enrolled. Eventually, the school reached the status as a full-fledged high school when it finally filled in students from the grades 9-12. The school is accredited by the Southern Association of Colleges and Schools.