Prince Charles and the Duchess of Cornwall visited a memorial and church outside the capital Kigali where the remains of victims are buried.
In 1994, ethnic Hutu extremists slaughtered hundreds of thousands of members of the Tutsi community.
The trip marks the first royal visit to Rwanda.
The Prince of Wales and the Duchess of Cornwall arrived in Rwanda on Tuesday night – one of a minority of nations the Queen has not visited.
Prince Charles is representing the Queen, the head of the Commonwealth, at the summit of Commonwealth leaders, which was postponed in 2021 and 2020 because of the pandemic.
He was encouraged to visit the National Genocide Memorial and museum at Gisozi by former Rwandan footballer Eric Murangwa.
He is the founder of the organisation Football For Hope, Peace And Unity, and was sheltered from the killings by teammates. The Prince of Wales made him an MBE in recognition of his efforts raising awareness of the genocide against the Tutsi.
The royal couple later held a meeting with Rwanda’s President Paul Kagame.
British Prime Minister Boris Johnson has confirmed that he will also travel to Rwanda to attend the summit.
Prince Charles’ visit comes after it was reported that the prince privately criticised the UK’s plan to send asylum seekers to Rwanda.
According to claims reported in the Times earlier this month, the heir to the throne was said to believe the policy was “appalling”.
The first flight due to take asylum seekers from the UK to Rwanda was cancelled last week, minutes before take-off, following legal rulings by Europe’s human rights court.
Prince Charles and Camilla were greeted on their arrival in Rwanda by a small group of dignitaries.
Among those greeting the royal couple at the steps of the plane were the UK’s High Commissioner to Rwanda, Omar Daair, Rwanda’s High Commissioner to the UK, Johnton Busingye, special adviser Yamina Karitanyi and the prime minister’s special representative on the Commonwealth, Lord Ahmad.