Activist Peter Krykant has been working with injecting users in the city since September.
Mr Krykant, who was charged under the Misuse of Drugs Act, is campaigning for a change in the law to allow the legal consumption of drugs such as heroin and cocaine.
He believes current laws force people to inject in squalid and dangerous conditions in alleyways, closes and waste ground.
The volunteer-run facility was allegedly operating in Glasgow’s Parnie Street.
The UK Government has previously rejected calls to legalise such facilities.
A Police Scotland spokesperson said: “A 43-year-old man has been charged in connection with an offence under the Misuse of Drugs Act 1971 on Parnie Street in Glasgow during the morning of Friday, October 23, 2020.
“A report will be submitted to the procurator fiscal in due course.”