Speaking to Russia's military top brass on Wednesday after watching the live feed of the launch of the Avangard system from the defense ministry's control room, Putin said the test was a "great success" and an "excellent New Year's gift to the nation".
According to the Kremlin, the missile was launched from the Dombarovskiy missile base in the southern Ural Mountains and hit its target on a test site in Kamchatka, about 6,000km away.
"The Avangard is invulnerable to intercept by any existing and prospective missile defense means of the potential adversary," Putin said after the test, adding that the new weapon will enter service next year with the military's Strategic Missile Forces.
The hypersonic missile was among the array of new nuclear weapons that Putin presented in March, saying that Russia had to develop them in response to the development of the US missile defense system that could erode Russia's nuclear deterrent.
When first presenting it, the Russian president said the new missile system has an intercontinental range and can fly in the atmosphere at 20 times the speed of sound, bypassing the enemy's missile defense.
He emphasized that no other country currently has hypersonic weapons.
Putin has said that Avangard is designed using new composite materials to withstand temperatures of up to 2,000 degrees Celsius that come from a flight through the atmosphere at hypersonic speeds.