Bob Njagi and Nicholas Oyoo went missing in October after travelling to the neighbouring east African nation to support Ugandan opposition leader Bobi Wine, who intends to run against long-time incumbent Yoweri Museveni in elections next year.
In a brief joint statement on X, rights groups Amnesty Kenya, Vocal Africa and the Law Society of Kenya (LSK) said they "welcome the release of Nicholas Oyoo and Bob Njagi last night in Busia after 38 days of their enforced disappearance".
The statement, posted by LSK head Faith Odhiambo, did not give any further details but said they were "facilitating their transfer to Nairobi".
It expressed thanks to human rights groups, as well as the foreign ministries, and active citizens who "tirelessly campaigned for this moment".
The pair went missing last month, with the Ugandan police denying either activist was in custody.
Rights groups and the men's families in Kenya have agitated for their return, appealing to the Uganda court and urging the government to disclose their whereabouts.
The head of Kenyan rights group VOCAL Africa, Hussein Khalid, said last month that eyewitnesses had reported that the two men were taken by "masked, uniformed and armed men, suggesting strong evidence of state involvement in their disappearance.
"It is our suspicion that the two may be detained alongside other Ugandan political detainees in military facilities," he said.
Dozens of government critics and opposition figures have been abducted in recent years across east Africa, and rights groups allege authorities are failing to protect their own citizens and even working together against activists.
In May, Kenyan activist Boniface Mwangi and Ugandan activist Agather Atuhaire say they were abducted and tortured by security forces in Tanzania, and received little support from their own governments.
