Flores was born in Corona, California.
Flores served as coadjutor bishop of San Diego from 2012-2013 and as auxiliary bishop of the Diocese of Orange from 2009–2012. He served as the bishop of the Diocese of San Diego in California. He held the position from September 18, 2013 until his death on September 6, 2014.
- "San Diego Bishop Cirilo Flores dies, battled prostate cancer". UT San Diego. 6 September 2014. Retrieved 6 September 2014.