At least once, yes.
He disapparates from the Ministry at the end of Order of the Phoenix, just as the Aurors and Fudge arrive:
“He was there!” shouted a scarlet-robed man with a ponytail, who was pointing at a pile of golden rubble on the other side of the hall, where Bellatrix had lain trapped only moments before. “I saw him, Mr. Fudge, I swear it was You-Know-Who, he grabbed a woman and Disapparated!”
— Order of the Phoenix, chapter 36, The Only One He Ever Feared
Of course, flying out of the Ministry is probably impossible.
At least on some occasions, Voldemort prefers to fly due to sheer distance. Harry sees this inside his head when he’s approaching Malfoy Manor in the final book:
Harry knew it; his scar was bursting with the pain of it, and he could feel Voldemort flying through the sky from far away, over a dark and stormy sea, and soon he would be close enough to Apparate to them, and Harry could see no way out.
— Deathly Hallows, chapter 23, Malfoy Manor
I don’t think the fact that both Harry and Voldemort prefer flying to apparition is anything except coincidence.