A judgment delivered by Justice Susan Thomas today granted the application, stating the case would "directly affect" CEC and the organisation would improve the quality of information before the court.
A condition of granting the application was that CEC would not be allowed to seek court costs.
Justice Thomas said it would be "disingenuous to suggest that Boards of Trustees will not take notice" of any decision.
McClintock's case did not originally include CEC because it was not the religious education provider at Red Beach Primary School.
His lawyer Richard Francois is seeking to repeal Section 78 of the Education Act, arguing the Red Beach Board of Trustees allegedly breached its duties under the Act, and that the Attorney General passed legislation inconsistent with the New Zealand Bill of Rights.
Mr Francois said the proposed inclusion of CEC was "intervening and ganging up" on Mr McClintock.
"This is a little man up against a giant - the Government with all its panoply of power," he said.
But CEC rejected the notion, arguing the case was "highly relevant" to the organisation.
It was implicitly challenging the rights of state school boards throughout the country to exercise discretion to allow voluntary religious education, CEC said.
The organisation provides religious education programmes to 667 state primary schools throughout New Zealand - about 80 per cent of state schools that allow Christian programmes.
Mr McClintock was disappointed at the decision because he said the CEC would only try to confuse the situation.
The Secular Education Network has been supporting Mr McClintock throughout the process.
Spokesman David Hines said the decision meant extra complications but it would be good to challenge the CEC's teachings in court.
"It's a great opportunity to have CEC's claims and its teaching material assessed by experts and the court," he said.
"We have, with difficulty, obtained some of this material and have handed it to a religious studies expert for comment."
