The 48-year-old is due to appear at Westminster Magistrates’ Court on September 6.
The MP for Dover was charged on Monday with three counts of sexual assault relating to two alleged victims, the Crown Prosecution Service said.
He is alleged to have attacked the first woman in 2007 and the second woman twice in 2016.
Elphicke denies any wrongdoing, will “defend himself vigorously” and is confident that he will clear his name, his lawyer said.
A source close to the MP told PA: “Charlie believes he has been fitted up – he has co-operated with this inquiry for 20 months.
“At the outset he gave them electronic and paper documents which proved the allegations were fabricated.
“He is stunned to have been charged, maintains 100% innocence and is confident he will be cleared.”
The Crown Prosecution Service (CPS) said Elphicke was charged after “reviewing a file of evidence from the Metropolitan Police”.
“The CPS reminds all concerned that criminal proceedings against Mr Elphicke are now active and that he has a right to a fair trial,” a statement said.
“It is extremely important that there should be no reporting, commentary or sharing of information online which could in any way prejudice these proceedings.”
Elphicke’s solicitor, Ellen Peart, a partner at BCL Law, said: “Charlie Elphicke has said from the outset that he denies any wrongdoing. He will defend himself vigorously and is confident that he will clear his name.
“Meanwhile Charlie would like to thank everyone for their continued support of him and his family.
“There will be no further comment at this stage.”
A senior Tory source said the Conservative whip was being suspended from the MP.
The move brings the working Tory-DUP majority in the Commons down to just two.
The next prime minister – either Boris Johnson or Jeremy Hunt – will face the prospect of that being further reduced to just one if the Tories lose the Brecon and Radnorshire by-election on August 1.
Elphicke had previously been suspended from the Conservative Party in November 2017 after “serious allegations” against him were referred to police.
Theresa May controversially restored the Tory whip to him 13 months later, in December, before she faced a vote of no confidence.
Mr Elphicke’s Constituency Association chairman, Keith Single, said: “Throughout the last 20 months since these allegations were first made, Charlie has had our full support.
“That support will continue. Basic British values require that everyone remains innocent until proven otherwise.
“Unfortunately, as everyone knows, there have been many recent occasions when, in dealing with matters of this type, the Metropolitan Police and the CPS have pursued allegations which have been proven in court to be entirely untrue.
“We have no doubt that this will be another one of them and Charlie will be fully exonerated.”
Elphicke, a former tax lawyer, has represented the Kent coast seat since 2010 – after the first alleged sexual assault – and was a Government whip under former prime minister David Cameron between 2015-16.