Richard Page, 70, was dismissed from his role when he made the comments on TV and was later sacked as an NHS Trust Director.
He will claim against Jeremy Hunt that he was discriminated against because of his religion.
Page was initially suspended and ordered to undertake "re-education training" in 2014 when he heard an adoption case and could not agree with colleagues that placing the child in the care of a same-sex couple would be in its interest.
Then in 2015 Page gave an interview to the BBC about freedom of religion where he reiterated his original position, saying: "My responsibility as a magistrate, as I saw it, was to do what I considered best for the child, and my feeling was therefore that it would be better if it was a man and woman who were the adopted parents."
He was then sacked by the then Lord Chancellor Michael Gove.
Subsequently he was dismissed from his role as an NHS Trust director amid claims his remarks had "undermined" the confidence of staff and patients.
Page will now take his case to an employment tribunal on the grounds of religious discrimination under the Equality Act 2010.
He is being supported by the Christian Legal Centre. Andrea Williams from the group told the Mail on Sunday: "Once again we find political leaders washing their hands of Christians prepared to stand up for their faith."
The Department of Health has been contacted for a statement.