The best option for Rwanda, Uganda and Kenya is the East Africa visa also called EATV. The visa is valid for all 3 countries with multiple entrée; also you can pass into Tanzania and come back (note: Tanzania is not included, you need to pay for that separately).
When we were traveling East of Africa by motorcycle we already applied online EATV visa and we paid more than what we were thinking. Because when we were applying we didn’t know that we could go to DRC, which country out of East Africa visa. So, just please read details and don’t do same mistake.
How to get the visa;
If your first enter is from Rwanda you can apply online and pay at the door. The costs are 100 USD (cash only in USD) for the visa. (If you want to have each countries cost will be 130 USD; Rwanda 30 USD single entry 30 days, Uganda 50 USD single entry 30 days and Kenya 50 USD single entry 30 days.)
For Uganda you need to apply online as well and you need to pay online too. The costs for the visa are now 103 USD as they charge 3% for the payment, you cannot pay on arrival
For Kenya you don’t need to apply online you can just get it on arrival at the bigger borders, you pay cash 100 USD for the visa.
The visa is valid for 90 days and you cannot extend it.
Important Note : If you leave from East African countries you lose your EATV. For example, You want to visit Virunga Park in DRC. When they put exit stamp on your EATV on the Rwanda border You cant turn back with same visa. You have to pay 30 USD to single entry visa to Rwanda or apply again online EATV. It is same for Ethiopia or Burundi as well.