The French president arrived in Moscow minutes after Merkel's plane touched down at Vnukovo airport and they headed straight to see Russian President Vladimir Putin.
Merkel and Hollande's mission is widely seen as a desperate attempt to prevent the 10-month conflict in eastern Ukraine from spiralling out of control as Washington is considering whether to send lethal weapons to Kiev.
Merkel arrived in the Russian capital for the first time since the Ukraine crisis began more than a year ago.
Hollande last travelled to Russia in December when he made a surprise stopover in a Moscow airport in an attempt to defuse mounting tensions over Ukraine.
Ahead of the Moscow trip the German leader played down hopes of a rapid end to the surging violence, while Hollande said the initial goal was a ceasefire.
"Everyone is aware that the first step must be a ceasefire, but that is not enough and there must be a comprehensive settlement," he told reporters ahead of his departure.
The French and German leaders were in Ukraine on Thursday night to meet President Petro Poroshenko to finalize a new initiative.
There, several ceasefires in recent months have failed to end the conflict, which has claimed more than 5,350 lives since April, including some 220 in just the past three weeks, according to the United Nations.
Hollande said at his biannual press conference on Thursday that Ukraine people needed to pitch in to end the war.
"It cannot be the said that we didn't do everything to preserve peace," Hollande said. "Peace is threatened on Europe's borders. Ukraine is at war."
He continued: "We think that war is for others, it's not for our generation, it's for our grand parents. But a few hours away from France by plane, there are men and women who dying every day.
"There are heavy weapons, artillery fire, there are hostilities," he said.