The French president arrived in Moscow minutes after Merkel's plane touched down at Vnukovo airport and they headed straight to see Putin.
"They are supposed to be going to the Kremlin now," a foreign ministry spokesman told AFP.
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.
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.