The Rochester Bridge Trust has transferred ownership of the Medway Tunnel to Medway Council and given the council £3.6m to spend on improvements and maintenance.
The 14th-century trust, which exists to maintain bridges at Rochester, has owned the tunnel since it was asked by Kent County Council to help in its construction in 1987.
But the tunnel, which links Strood and Chatham, has been run by Kent County Council, and subsequently Medway Council, although the trust has made an annual donation towards its maintenance.
Dr Anne Logan, senior warden of the trust, said it made no sense for the trust to own the freehold and the transfer would remove an unnecessary layer of bureaucracy.
The trust said that although the payment to the council will reduce its reserves and have a "long-term negative effect" on interest payments used to maintain other bridges, the charity's viability was not in question.