Parliaments in all 30 members of the military alliance must formally ratify Finland and Sweden before they can be admitted. Turkey and Hungary are the only two NATO members not to have done this.
Stoltenberg's comments come after Turkey suggested it could greenlight Finland's bid to join without accepting Sweden into the alliance.
"So the main question is not whether Finland and Sweden are ratified together. The main question is that they are both ratified as full members as soon as possible," Stoltenberg said ahead of a meeting of NATO allies.
"I'm confident that both will be full members and we are working hard to get both ratified as soon as possible," the NATO secretary general added.
Finland and Sweden dropped decades of military non-alignment and applied to join NATO in May last year in response to Russia's invasion of Ukraine.
But Turkey has so far refused to ratify the two countries' membership bids, primarily because of Sweden's refusal to extradite dozens of suspects that Ankara links to outlawed Kurdish fighters and a failed 2016 coup attempt.
Ankara reacted with fury to a decision by the Swedish police to allow a protest at which a far-right extremist burned a copy of the Koran outside the Turkish embassy in Stockholm last month.
Turkish President Recep Tayyip Erdogan has drawn a clear distinction between the positions taken by Sweden and Finland in the past few months and said "we can give a different response" to Helsinki.
Finland insists its "strong desire" remains to join NATO together with Sweden.
But a majority of Finns said in a poll this month that they wanted to join NATO even if Sweden's membership was delayed.
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