He served as a fighter pilot at the 5th Main Jet Base in Merzifon between 1966 and 1970 and at the 9th Main Jet Base in Balıkesir between 1970 and 1974.
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After his graduation from the Air War College in 1976, Babaoğlu has been assigned to the 4th Main Jet Base in Ankara, where he served in different positions including Squadron Commander.