Ferhan Çeçen was born on June 15, 1961, in Istanbul, Turkey. She graduated from the Deutsche Schule Istanbul in 1980 and speaks fluent English and German in addition to her native Turkish. Çeçen completed a B.S. in chemical engineering at Boğaziçi University in 1984.
In 1986, she completed a M.S. in environmental engineering at the Istanbul Technical University (ITU). Her Masters thesis was titled Metal Complexation and its Implications on related Technologies'. Her graduate advisor was .
Çeçen earned a Ph.D. in environmental engineering at ITU in 1990. Her dissertation was titled Nitrogen Removal from High-strength Wastewaters by Upflow Submerged Nitrification and Denitrification Filters. Her doctoral advisor was .