Ms McGarry, who has resigned the SNP whip but remains MP for Glasgow East, was also a leading figure in the Yes campaign for Scottish independence.
The Scotsman understands that the charges are connected to the finances of the Women for Independence organisation and the Glasgow regional association of the SNP.
A statement released by Police Scotland said: “On Tuesday September 27 a 35-year-old woman was charged in connection with alleged fraud offences.
“A report will be sent to the procurator fiscal.”
Ms McGarry has always maintained her innocence, ever since it emerged that she was at the centre of a police investigation.
The investigation was launched after a complaint was made to Police Scotland by members of WFI’s national executive committee in November 2015.
Ms McGarry withdrew from the SNP whip when the matter was reported to police.