So I read on the State Department website that you don't need to YF vaccine for Rwanda, unless arriving from a country where YF is endemic. So I'm confused as to what exactly counts as "arriving from". Because I was thinking about transiting through Uganda, where YF is endemic, and I originally thought I would be exempt from YF vaccine, if I'm only transiting. But then it dawned on me that if I end up having to clear customs in Uganda, and get my passport stamped, how will I proof to Rwandan officials that I didn't actually leave the airport? So basically my question is, do I still need a YF vaccine for Rwanda, if I'm not actually leaving the airport in Uganda?

When I was on a trip that required a YF vaccination a medical waiver was given with a letter from my doctor. While looking for that online I ran across this: ". . . under 12 hours of airport transit the risk of yellow fever is almost non‐existent and therefore a proof of vaccination might not be necessary." So it appears to be a question not of where you are (airport or ?) but how long you're there. You'll have to ask about Rwanda's rules in that regard.

ith_country_list.pdf

However, if the information on that link is current, it also has this:
"RWANDA: Yellow fever country requirement: a yellow fever vaccination certificate is required from all travellers over 1 year of age. Yellow fever vaccine recommendation: yes

So, again, I'd look for current information from Rwanda, a consulate probably.