If successful it will be the longest journey to date for the craft after an inaugural flight to Paris and Brussels last year.
Organisers announced at the end of March that the 2,500 km (1,550 mile) trip will coincide with the launch of construction on the largest ever solar thermal plant in Morocco's southern Ouarzazate region.
The plane is scheduled to take off from a military airport at Payerne in Switzerland at 06:45 am, piloted by Andre Borschberg, who is expected to land in Madrid at around 2:00 am on Friday for a stopover.
Bertrand Piccard will pilot the second leg on to Rabat, scheduled to leave Madrid on Monday at the earliest, organisers said.
In Morocco, Solar Impulse will be welcomed by the Moroccan Agency for Solar Energy (MASEN).
The trip would be a rehearsal in the run-up to the plane's round-the-world flight planned for 2014.
The high-tech aircraft, which has the wingspan of a large airliner but weighs no more than a saloon car, made history in July 2010 as the first manned plane to fly around the clock on the sun's energy.
It holds the record for the longest flight by a manned solar-powered aeroplane after staying aloft for 26 hours, 10 minutes and 19 seconds above Switzerland, also setting a record for altitude by flying at 9,235 metres (30,298 feet)