Discussions between the German leader and Clooney, as well as his wife Amal -- a Lebanese-born human rights lawyer -- focused on "refugee policies and their involvement in the IRC" -- aid group International Rescue Committee, Merkel's spokesman Steffen Seibert wrote on Twitter.
Britain's former foreign minister David Miliband, who is now head of the IRC, also attended the discussions, Merkel's spokeswoman Christiane Wirtz added.
"There was an exchange on refugee policy as well as issues surrounding international conflicts during the meeting which was held at the request of Mr and Mrs Clooney," she added.
The actor had told reporters on Thursday that he would meet Merkel and, separately, a group of asylum seekers, "to talk about and ask what messages and what things we can do... to help."
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Germany took in around 1.1 million asylum seekers in 2015 alone, but opposition is growing within the country against Merkel's liberal policy.
An opinion poll published late January showed that nearly 40 per cent of German voters want Merkel to quit over her asylum policy.
Newspaper Berliner Zeitung warned that Merkel's meeting with Clooney "could backfire" on her.
"As the chancellor is meeting an actor at a time when there is falling confidence on her migration policies, she could be reproached for preferring to bask in the glow of Hollywood rather than solving the country's urgent problems," it said.