The new application forms do not distinguish between gay or straight marriages.
The department also said students' eligibility for federal aid would be the same in all 50 states, regardless of where the student attends school.
For instance, a same-sex couple from Massachusetts, where gay marriage is legal, would be treated the same as a straight couple if one or both applied for a federal loan to attend a school in one of the 34 states that do not permit gay marriage. The same standards would apply to parents in same-sex marriages.
"As students fill out their FAFSA this coming year, I'm thrilled they'll be able to do so in a way that is more fair and just," Duncan said, using the financial aid application's acronym.
The change was formally announced to colleges and parents in a letter from Brenda Dann-Messier, the department's assistant secretary for vocational and adult education.
Before the Supreme Court ruled this summer, the Education Department was bound by the Defense of Marriage Act, which prohibited all federal agencies from recognizing same-sex marriages. The Clinton-era law defined marriage as between one and one woman and worked against many applicants in same-sex marriages.
Friday's move is the latest effort by the Education Department to be more helpful to students in same-sex marriages, and those with married gay parents.
Even before the ruling, Duncan instructed the department to collect information on both of the student's legal parents, regardless of marital status. That meant children being raised by unmarried couples - regardless of sexual orientation - would have both adults' incomes factored into financial aid eligibility.
That was done to reflect that same-sex couples share financial responsibilities for children, even if their state does not sanction gay marriages.