It was in August that Trump stated that he fired her, and claimed that she had not handled her mortgage applications correctly. Cook's lawyers have previously called the dismissal illegal and said that it lacks grounds.
The ruling means that Cook will be able to remain in her position at the central bank until the lawsuit has been dealt with by the court in its entirety.
The court decision is the latest step in the conflict between the White House and the central bank, where Trump demands a lower interest rate but the Fed asserts its independent decision-making power.