The Church made the demand as Scotland's Equality and Human Rights Commission considers its guidance notes for gay marriage, which becomes legal on December 31, 2014 in Scotland.
The Free Church says it doesn't want pupils "forced" to listen to "controversial teaching" on gay marriage, suggesting it would be in "direct opposition" to the strongly held religious beliefs of some.
Elsewhere in its submission the Free Church said it was worried that some of the guidance could threaten freedom of speech, because freedom of expression hinged on "forms of words" or "contexts" - adding that individuals will be intimidated by the fear that their comments could be construed to have crossed an "invisible line".
It also criticised the "one-sided nature" of the proposed guidance, and suggested that gay lobby champions who brand supporters of traditional marriage "bigots" or "homophobic" should face similar sanctions to those who make derogatory remarks about same-sex relationships.
Rev James Maciver, Principal Clerk of the Free Church's General Assembly, said: "We urge the Scottish Government to extend the right to withdraw pupils to cover all lessons designed to promote same-sex marriage as a morally acceptable marriage form.
"This inequality of having no opt-out for lessons in which same-sex marriage will be presented, should be resolved."
A EHRC spokesman said: "We are in the process of considering the large number of responses received, including the response from the Free Church of Scotland. We hope to publish the guidance by the end of the year.
"As you'll appreciate, it would not be appropriate to publicly comment on one organisation's consultation response at the moment."
