Mr O’Mara was charged in connection with allegations that he made fraudulent invoices to the Independent Parliamentary Standards Authority in 2019.
The former MP was elected as a Labour candidate for Sheffield Hallam in 2017 before sitting as an independent until he stepped down two years later.
He is due to appear in front of Sheffield Magistrates’ Court in September.
The CPS said that Mr O’Mara had been charged alongside his former aide, Gareth Arnold, who faces six counts of fraud by false representation.
Mr O’Mara and a third man, John Woodliff, have also been charged with a Proceeds of Crime Act offence, they added.
All three men will appear before the magistrates’ court on 24 September.
Rosemary Ainslie, head of Special Crime at the CPS, said: “The CPS made the decision that the three men should be charged after reviewing a file of evidence from South Yorkshire Police.
She added: “The CPS reminds all concerned that criminal proceedings against these defendants are active and that they have a right to a fair trial.
“It is extremely important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings.”
The Independent Parliamentary Standards Authority regulates MPs’ expenses as well as their pay and pensions.
Mr O’Mara won his Sheffield Hallam seat from former Lib Dem leader Nick Clegg in 2017 after running as a Labour candidate.
However, after being suspended from the party over the emergence of offensive comments he had made online, he sat as an independent.
He was later reinstated to the party – although he disputes that this happened – but resigned and continued to serve as an independent until stepping down from his post at the December 2019 general election.
He was succeeded by Labour MP Olivia Blake.