The start-up of a scheduled air transport line with the Peninsula was a long-standing aspiration of the authorities in the autonomous city of Ceuta, due to the communication difficulties when adverse sea conditions in the Gibraltar Strait prevented the use of the ferries linking Ceuta with Algeciras.

Answering this claim, the General Staff of the Army awarded temporary authorisation in January 1996 for the civil use of its facilities. The success of this initiative among the civil population of Ceuta and the limited time of the authorisation lead, in January 1998, to an initial study for the establishing of a permanent commercial facility open to civil traffic. This project was finally included in the Ministry of Economic Development Transport Infrastructure Plan 2000-2007, which awarded the construction and maintenance to Aena that, in July 2002, had to modify its statutes to be able to expand its management to aerodromes, heliports and other areas suitable for air transport.

Given the impossibility, for orographic reasons, to site an airport on the outskirts of Ceuta, the solution of a heliport arose. To be able to complete the project, a suitable location had to be sought: not an easy task due to the scarcity of ground in the autonomous city and to the large number of military areas.

Finally the port of Ceuta was chosen, placing the new facilities next to the urban centre to avoid long trips by the operating companies and their passengers. Due to the fact that the military heliport had no boarding area, until then passengers had to be checked in an especially equipped area in the port and were then taken by van to the military facilities for boarding.

Once the site at the fishing port had been chosen, the physical requirement of designing a civil heliport to comply with ICAO normative was approached, for which an additional area over the water of the port was required.

Following negotiations with the port authorities, the heliport work began in the year 2000 and was completed in 2003, although as established in the Infrastructure Plan 2000-2007, the continuous improvements will continue until beyond 2010. Ceuta heliport was officially inaugurated by the Secretary of State for Infrastructures, Benigno Blanco, on 9 January 2004.