For more than a month thousands of displaced people have been stuck in DR Congo’s Ituri region trying to seek safety in northern Uganda.
The government in Kampala finally agreed to give them entry on humanitarian grounds.
They will first spend 14 days quarantined at a newly set-up isolation centre, 13km (eight miles) from the border.
The UN’s refugee agency says sample testing will be carried out on the group to see if coronavirus is present amongst them.
This will help authorities decide when they can be transferred to camps.
Aid agencies have talked about the difficulties of ensuring social distancing and sanitation in refugee settlements.
Fifty-two refugees have so far tested positive for Covid-19 in Uganda out of nearly 900 confirmed cases.
The UN says it is concerned about reports of rising violence in the DRC, where five million people are internally displaced.
UN soldiers patrol violence-torn eastern DRC in March 2020.