The bill passed both houses of the New Jersey Legislature with bipartisan support in June. Assemblyman Tim Eustace, who sponsored the bill and is openly gay, described the therapy as "an insidious form of child abuse."
Gay activists pushing the ban were uncertain what Christie would do.
In a signing note accompanying the bill that will be made public Monday, Christie said he believes people are born gay and that homosexuality is not a sin. That view is inconsistent with his Catholic faith.
The Republican governor also said the health risks of trying to change a child's sexual orientation, as identified by the American Psychological Association, outweigh concerns over the government setting limits on parental choice.
"Government should tread carefully into this area," he said in the signing note, which was obtained by The Associated Press, "and I do so here reluctantly."
"However, I also believe that on the issues of medical treatment for children we must look to experts in the field to determine the relative risks and rewards," Christie said, citing a litany of potential ill effects of trying to change sexual orientation, including depression and suicide. "I believe that exposing children to these health risks without clear evidence of benefits that outweigh these serious risks is not appropriate."
Gay rights groups say the practice is damaging to young people because it tells them that it's not acceptable to be whoever they are.
Some social conservatives framed the debate as a parental rights issue, saying a ban on the counseling would limit the ability of parents to do what they think is best for their children.
The idea of conversion therapy is an old one that has increasingly drawn criticism for its methods. Last year, four gay men sued a Jersey City group for fraud, saying its program included making them strip naked and attack effigies of their mothers with baseball bats.
Lawmakers heard horror stories from some during hearings on the ban, including Brielle Goldani of Toms River, who testified she underwent electric shocks and was given drugs to induce vomiting after being sent to an Ohio camp at age 14 to become straight.
But, they also heard from Tara King, a Brick-based counselor, who said she should be allowed to "fix" what patients, even under-aged clients, want fixed.