On Tuesday, Obama reversed plans to withdraw around 5,000 US troops from Afghanistan this year after talks with the country's new, reform-minded leader, President Ashraf Ghani.
"I welcome President Obama's decision to extend the period where US forces will remain close to 10,000 troops in Afghanistan," Stoltenberg told reporters at a Washington press conference.
"It's a sign of flexibility that confirms the strong commitment of the US and NATO in Afghanistan," Stoltenberg added.
Nonetheless, NATO personnel remain in the country in a training and advisory capacity.
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In explaining the slowed troop withdrawal, Obama said he wanted to do everything possible to help Afghan security forces succeed in the country where some 2,300 US soldiers died between 2001 and 2014.
On a working visit to the US capital, Stoltenberg, in office since October 2014, wasn't received by Obama.
Asked about that, the secretary general said he'd met with Obama in the fall.