Alfred Chan Cheung-ming over from incumbent chairman York Chow Yat-ngok starting April 11 for a term of three years.
The news has been met with derision by LGBT advocacy groups including Pink Alliance who expressed "disappointment" a the announcement.
Chow had been criticised by anti-gay groups for his vocal support of LGBT rights, though Pink Alliance described him as having "dutifully exercised its mandate" under his leadership.
Alfred Chan Cheung-ming has served as chairman of the Elderly Commission since 2011 and Lingnan University social policy professor.
"Professor Chan's clear vision, passion and commitment in various areas of equal opportunities have been fully evidenced by his work and experience in the social service and tertiary education sectors over the years," a government spokesperson said.
"[He] has extensive experience in public service and possesses good leadership, management and communication skills. We are confident that under his leadership, the EOC will continue to actively promote equal opportunities and eliminate discrimination in the community."
The EOC, under Chow's leadership, made headlines this year when a study it commissioned found that more than half of Hongkongers surveyed are in favour of legislation against sexual orientation, gender identity and intersex status discrimination, which was subsequently ignored by the Government.