Clinic26 will provide sexual health services and emotional support to men of all ages at the Ambrose Centre at the Royal London Hospital.
On average, 12,000 men are raped and 72,000 are sexually abused each year, Home Office statistics show.
The clinic has been set up in partnership with Survivors UK.
One sexual abuse victim said he was thrilled when he heard the clinic was opening.
Jay - not his real name - said he was sexually assaulted by a nurse when he had a routine health screening in 2013.
"I was hugely distressed by it (the assault). It took me nine months to go back for another screening," he said.
Initially, the health trust did not take action against the nurse, but it eventually reinvestigated before another victim came forward. The nurse was found guilty and was jailed for two years.
Jay said he wanted to go to a place "where people knew" he'd been sexually assaulted and he didn't have to disclose it to see the reaction.
Andy Williams, consultant physician at The Royal London Hospital, said: "We need to break the taboo that allows men to suffer in silence and this clinic is the beginning of what we hope will be a valued support resource for men in east London."
Alan Robertson, Independent Sexual Violence Advisor at Survivors UK, said: "Going to a sexual health clinic can be a daunting prospect for anyone, but especially so for someone who has experienced trauma or an abuse of power."
The clinic will run on the afternoon of the last Monday of each month.
Support groups have set up what they say is the first UK clinic to offer support for male sexual abuse victims.