Gay marriage became legal in the country on May 1st, allowing couples to wed in religious or civil ceremonies.
Until now, the church had not decided whether to allow them to marry in church.
In June, the church board submitted a petition to the Church of Sweden synod. The synod announced the decision this morning.
According to The Local, some small changes will be made to current church regulations, such as replacing “man and wife” with “lawfully wedded spouses” when gay couples marry.
In January 2007 the church, which was disestablished in 2000, began offering religious blessings to gay unions and actively welcomed LGBT clergy.
Six of the seven political parties in Swedish parliament backed the proposal to introduce a gender-neutral marriage law.
The proposal passed with a 261 to 22 vote and 16 abstentions.
The only party to oppose the ruling were the Christian Democrats, who said they wanted to maintain "a several hundred-year-old concept" of marriage.