"The federal government is responding to the arrival of record numbers of individuals, including unaccompanied children, at the southwest border", the department said.
Children began pouring over the border after President Biden took office, mostly due to his more relaxed stance on the border.
House Speaker Nancy Pelosi (D-Calif.) blamed Republicans for the sudden surge of migrants at the southern border, even though Democrats control the White House and both chambers of Congress.
Hundreds continue to arrive each day, and many are being held beyond the legal three-day limit after which they are supposed to be turned over to health officials who find homes for them while their immigration case is resolved.
The Department of Homeland Security said in a statement that Fema would be part of a 90-day effort to ensure the children are safely sheltered and transferred to people who will take care of them, usually relatives already living in the United States.
One administration official said the 2018 policy had a "chilling effect" on parents and sponsors who were anxious about coming forward to claim their children, and added, "There will not be immigration consequences going forward". During that crisis, Fema helped stand up temporary shelters and processing stations on military bases.
Announcing Fema's involvement, Mr Mayorkas said the agency would work with the Health and Human Services Department (HHS) to "look at every available option to quickly expand physical capacity for appropriate lodging".
More than 4,000 unaccompanied migrant children are in Border Patrol custody - yet another increase stressing an unprepared system.
FEMA was also called in to help in 2014 when a similar influx of unaccompanied minors occurred under former President Barack Obama.
According to the Biden Administration, the president is working to find a balance between promoting a more humane approach to immigration while still sending the message to would-be migrants not to come. Biden is eliminating the "Remain in Mexico" policy that ordered asylum seekers to wait in Mexico while their cases were processed in the US, and the administration has reinstituted "catch-and-release" policies, in which border agents release migrants into USA border towns to await processing.