Chief Constable Serena Kennedy Merseyside Police in England issued the statement in response to a letter sent last year by the human rights campaigner Peter Tatchell.
She offered her “sincere apology and deepest regret” for “historical prejudice” to older members of the community.
Mr Tatchell had urged all police forces in the UK to apologise for “decades long victimisation” of LGBT+ people, particularly in the 1980s and 1990s.
Ms Kennedy said the force’s response followed a period of “extensive consultation” with representatives from the local LGBTQ+ community.
She wrote: "With this apology I acknowledge the harm, unique impact, and the erosion of trust and confidence that resulted for them.
“Our mistreatment had the ripple effect across the whole LGBTQ+ community and the impact on their relationship with Merseyside Police.”
Merseyside Police became the 18th UK force to recognise homophobic victimisation after Mr Tatchell’s campaign, including the Met, Dorset and North Yorkshire. Ruined lives
On receipt of the letter, Ms Kennedy said she had “immediately recognised the need to address past injustices and acknowledge the harm caused by over-zealous policing and behaviour, policies and processes that enabled homophobia to thrive at that time”.
The force said it acknowledged that the “homophobic application” of legislation in place at the time was wrongly used to target, in particular, gay and bi-sexual men.
It said the impact ruined lives and prevented LGBTQ+ people from living openly for fear of prison.
Ms Kennedy said she was “extremely grateful” to people who shared their “traumatic experiences” with Merseyside Police over the last 12 months.
She added she was committed to “ongoing consultation” to further understand the impact and to ensure “we continue to learn from our mistakes”.
The force said it now worked closely with LGBTQ+ representatives on both recruitment of officers and promoting the reporting and prevention of hate crimes.