Domestic legislation, which will be rushed through Parliament to assert Rwanda is a safe destination for asylum seekers who arrive in Britain, is also planned.
Mr Cleverly will meet his counterpart, Vincent Biruta, to sign the treaty and discuss key next steps on the so-called migration and economic development partnership.
He also visited the genocide memorial in Kigali on Tuesday morning, during his first overseas visit as home secretary.
Ministers hope the upgraded agreement, along with “emergency” legislation at home, will address the issues that led the UK’s highest court to rule the Rwanda scheme unlawful.
“We are clear that Rwanda is a safe country, and we are working at pace to move forward with this partnership to stop the boats and save lives,” Mr Cleverly said before his arrival.