Johnson has been accused of misconduct in public office after making the claim during the 2016 EU referendum campaign, the BBC reported.
A judge at Westminster Magistrate's Court in London ordered that the former Foreign Secretary must face private summons on three counts of misconduct in public office.
Johnson had falsely claimed Britain's membership of the EU cost £350 million a week and it was plastered on the side of a bus that toured Britain during the campaign that resulted in 52 per cent vote in favour of the UK leaving the EU.
Campaigner Marcus Ball brought a private prosecution against Johnson, saying he misled the public in the run-up and aftermath of the referendum and repeated the £350 million claim during the 2017 elections.
Ball, who denies he is trying to obstruct Brexit, has raised more than £200,000 for the private prosecution through crowdfunding.
"Having considered all the relevant factors, I am satisfied that this is a proper case to issue summons as requested for the three offences as drafted," wrote Judge Margot Coleman. "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."
Johnson called the case a "political stunt".
In his deposition, he said: "The 'Prosecutor' (a limited company) is 'Brexit Justice Limited'. Brexit Justice Limited is the product of a campaign to undermine the result of the Brexit referendum, and/or to prevent its consequences.
"The company and this application owe their existence to the desire on the part of individuals such as Ball to undermine the referendum result. The 'Brexit justice' which is ultimately sought is no Brexit."
Johnson's lawyer Adrian Darbishire said the statements were made for the purpose of a political campaign and came from "freely available" information.
( With inputs from IANS )