A spokeswoman for the Crown Office, which is responsible for the prosecution of crime in Scotland, confirmed that Jamie Rennie, 37, had been charged with possession of indecent images of children.
She said Rennie had been committed for trial after being remanded in custody but that no date for his next appearance had been set.
The national board of LGBT Youth Scotland has issued a statement saying: "LGBT Youth Scotland has been made aware by Lothian and Borders Police that Jamie Rennie has been arrested in connection with the investigation of a serious offence. We have acted immediately to suspend Jamie Rennie as chief executive pending the outcome of police investigations."
LGBT Youth Scotland works towards the inclusion of lesbian, gay, bisexual and transgender young people in Scotland.
Rennie joined the organisation 11 years ago after becoming involved in Stonewall Youth.
