It was built along with Cypress Ranch High School and opened in fall 2008.

The rapid growth in CFISD prompted the district to schedule the opening of the school in fall 2008.

The school's first principal, Sarah Harty, was a former principal of Cypress Springs High School; she moved from Cy Springs to Cy Lakes upon the opening of the latter.

[3] On March 28, 2014, former Houston Rockets center Dwight Howard visited the students at Cypress Lakes High School for winning the "Block Out Violence" program.

The school received one of the seven possible distinction designations for Top 25%: Comparative Closing the Gaps.