Sudan has one of the most expensive and complicated visa application processes. Not sure I completely understand the process but luckily The hotel arranged everything for us.
Firstly, everyone needs a visa except Egyptians and they won’t issue you a visa if you have evidence i.e. a stamp in your passport, indicating that you have visited Israel. Some hotels can arrange a “counter visa” in advance so that you can collect this at the airport on arrival. With this you will be required to make a payment of $100 ($150 for US citizens because they’re wealthier?), have a photo and finger prints taken and a formal visa placed in you passport. Simple… But not over yet.
You now have to register within 3 days at the Aliens Registration Office at a further fee, with 2 passport photos and copies of your passport. The hotel did this for us at a fee of SDD 300 (+-$70).
And lastly, a travel permit is required for most journeys outside Khartoum, excepting northern destinations. You need to take two photos, a copy of your passport and SDD8700 to the Ministry of Humanitarian Affairs. It usually takes a day or two. You must make copies of this because the police will request it at check points. Again this was done for us.