Councillor Alan Donnelly was suspended by the Scottish Conservatives earlier this month as police launched an investigation.
The alleged incident happened at Trinity Hall in Holburn Street, Aberdeen, in November last year.
Mr Donnelly represents the Torry and Ferryhill ward on the Conservative and Labour-ruled council, and has been in post for more than a decade.
A police spokesman said: “Police Scotland can confirm a 64-year-old man has been arrested and charged in connection with an alleged sexual assault.
“The incident happened in November 2018 at Trinity Hall, Holburn Street, Aberdeen, and was reported to police in January 2019, when an investigation began.
“A report will be submitted to the Procurator Fiscal.”