Mr Mattis said in a statement he would set up a panel of experts serving in the Departments of Defense and Homeland Security to provide recommendations on implementing the ban.
He said he would advise the president after the panel reports it recommendations, and "in the interim, current policy with respect to currently serving members will remain in place".
Mr Trump signed a memorandum on Friday directing the U.S. military not to accept transgender men and women as recruits and halting the use of government funds for sex-reassignment surgeries for active personnel unless the process is already under way.
A White House official who briefed reporters about the memo on Friday declined to specify whether transgender men and women who are currently active in the military could continue to serve based on such criteria.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The memo called on Mr Mattis to submit a plan to Trump by Feb. 21, on how to implement the changes.
Mr Mattis said he expects to issue other guidance "including any necessary interim adjustments to procedures, to ensure the continued combat readiness of the force until our final policy on this subject is issued".
Mr Trump's directive created uncertainty for thousands of transgender service members, many of whom came out after the Pentagon said in 2016 it would allow transgender people to serve openly.
The decision appealed to some in Mr Trump's conservative political base while drawing criticism from advocates of lesbian, gay, bisexual and transgender (LGBT) rights.
Civil rights groups filed two new lawsuits on Monday challenging Mr Trump's ban.
