The favourite to win the Tory leadership race faces a private prosecution by campaigner Marcus Ball.
Lawyers representing Mr Ball lodged an application to summons Mr Johnson to court, claiming he had deliberately misled the public during the Brexit referendum campaign in 2016 and then repeated the statement during the 2017 general election.
In a written decision, District Judge Margot Coleman said Mr Johnson will be summonsed to court.
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She wrote: "The allegations which have been made are unproven accusations and I do not make any findings of fact.
"Having considered all the relevant factors I am satisfied that this is a proper case to issue the summons as requested for the three offences as drafted. The charges are indictable only.
"This means the proposed defendant will be required to attend this court for a preliminary hearing, and the case will then be sent to the Crown Court for trial.
"The charges can only be dealt with in the Crown Court."
Mr Ball has raised more than £200,000 through a 'Brexit Justice' crowdfunding campaign to pay for the private prosecution.
The decision to summons the former foreign secretary was criticised by Tory Brexiteer Jacob Rees-Mogg, who said it was a “troubling” abuse of process.
He said: “It is trying to use the courts to achieve a political end which, I think, is neither right or proper. This is involving the courts in something that is not their area.
“We need courts and politicians to respect each other, and it is an abuse of process, and a troubling one. It has been brought by people who are resentful of the referendum result.”