The Crown Prosecution Service said the charges relate to allegations he made fraudulent invoices to the Independent Parliamentary Standards Authority in 2019.
He is charged alongside former aide Gareth Arnold, who faces six counts of fraud by false representation.
The CPS said O’Mara and John Woodliff were also charged with a Proceeds of Crime Act offence.
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.
“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.”
O’Mara stepped down as MP for Sheffield Hallam in 2019. He won the seat for Labour in 2017, but later quit the party and held it as an Independent.
His former office manager Gareth Arnold originally announced his intention to stand for election in the seat in the 2019 election, but later withdrew after securing another role and did not take part in the ballot.