ACM Prajin informed the THAI board on Thursday about the decision to step down, saying he also sat on the 17-member super-board to revamp struggling state enterprises.
Vice-chairman Areepong Bhoocha-oom has temporarily taken over the post until a new chairman is selected.
ACM Prajin did not deny the possibility of sitting in cabinet and said he could be assigned to handle the Energy Ministry.
THAI has struggled since last year and is expected to be in the red again this year.
The state enterprise and its subsidiaries posted a net loss of 7.65 billion baht in the second quarter, down from 6.88 billion baht in the same period of last year, it said in a statement released on Thursday.
Decreasing tourist arrivals due to the impact of the political unrest and rising competition from low-cost airlines had hampered its operations, the airline said.
Acting vice-president Surapol Isarakura na Ayutthaya said on Friday the airline expected a 10 billion baht loss this year.