"We have forces here 365 days a year," Scaparrotti told Vilnius journalists.
"I want some flexibility on that so it may not be but it will be nearly that if not that because of the forces we have," he added.
In response to the Russian intervention in Ukraine, the United States has been deploying about 150 troops in each of the Baltic states since 2014. A brigade of US troops was stationed in Poland earlier this year.
Scaparrotti said that the battalion of US troops would rotate in Lithuania in June and July, as well as attend the exercise Saber Strike.
He also noted that another US battalion would be rotated in the Baltic states in September, the month Belarus and Russia hold a large-scale exercise Zapad 2017.
"The geopolitical situation in Europe remains tense, while the big neighbor continues rattling sabers," Lithuania's Chief of Defence Lieutenant General Jonas Vytautas Žukas told the news conference.
"During the meeting, I expressed an expectation to see US troops in Lithuania both before the Russian training Zapad 2017 and after it," he added.
This year, a battalion-sized unit will be stationed in each of the Baltic states. The battalion in Lithuania will be headed by Germany.
Lithuania's officials have lately repeatedly urged the United States to station its forces on a permanent basis in the region to ensure faster deterrence of Russia.
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