The new policy, which will allow troops to transition gender while serving and set standards for medical care, will now come into effect on 1 January 2018.
Pentagon officials say that different services are not in agreement about when to accept recruits.
Rights activists have said they are disappointed with the delay.
"Each day that passes without the policy in place restricts the armed forces' ability to recruit the best and the brightest, regardless of gender identity," said Human Rights Campaign spokesman Stephen Peters in a statement.
Mr Mattis said in a memo quoted by the Washington Post he had decided more time was needed to make a decision after consulting senior defence officials, adding that the delay "in no way presupposes an outcome".
Pentagon spokeswoman Dana White said in a statement that the delay was imposed so the armed services could "review their accession plans and provide input on the impact to the readiness and lethality of our forces."
A study by the Rand Corporation last year, commissioned by the military, estimated that there were between 2,500 and 7,000 transgender active service members in a total force of 1.3 million, with an additional 1,500 to 4,000 among reserve units.
The Palm Center, an influential think tank which studies gender in the military, estimates that there are about 12,800 transgender service members.
Under the shelved plan drawn up by former defence secretary Ash Carter, transgender individuals would be able to enlist as long as they had been "stable" in their identified gender for 18 months.
US Defence Secretary James Mattis has approved a six-month delay to an Obama administration plan to let transgender recruits into the US military.