More than 10,000 people have been killed since a Russian-backed rebellion against the pro-EU government in Kiev erupted in April 2014.
Ukraine and the West accuse Moscow of smuggling weapons and troops across the porous border, a charge it denies, AFP reported.
"Russia has maintained its aggressive actions against Ukraine, but NATO and NATO allies stand by Ukraine and stand on your side," Stoltenberg said in his opening remarks of the NATO-Ukraine Commission session in Kiev.
The conflict in eastern Ukraine and Russia's annexation of the Ukrainian peninsula of Crimea in 2014 have driven ties between Moscow and the West to their lowest point since the Cold War.
"We are also here to demonstrate NATO's solidarity with Ukraine and our firm support for the sovereignty and territorial integrity of your country," Stoltenberg said.
"NATO allies do not and will not recognize Russia's illegal and illegitimate annexation of Crimea."
The NATO chief's visit came a day after US Secretary of State Rex Tillerson made a maiden visit to Kiev and urged Moscow to take the "first step" to ease the conflict in Ukraine's east.
The US and the European Union have imposed sanctions on Russia, though Moscow has denied backing the rebels.
Ukraine sees NATO accession as a way to bolster its defenses against former master Moscow.
In June, Ukraine's parliament voted to back attempts by the nation to seek membership of the 29-member bloc.
It approved legal amendments enshrining membership in NATO as a foreign policy priority.
However, Kiev has yet to officially apply to start the lengthy and politically challenging process of joining the alliance.