Goodell wrote to all 32 NFL teams on Tuesday following weeks of controversy surrounding the large number of players who have protested against perceived racial injustice by taking a knee during the anthems. A copy of the memo was published on NFL.com.
On Sunday, US vice president Mike Pence walked out of the Indianapolis Colts' game against the San Francisco 49ers after a large number of 49ers players took a knee during the anthem.
Goodell has previously defended the rights of players to express their feelings, but said in his memo that the controversy was overshadowing the issues they were seeking to raise.
In the memo, Goodell said: "The current dispute over the National Anthem is threatening to erode the unifying power of our game, and is now dividing us, and our players, from many fans across the country."
He added that the league had discussed the protests with team owners and players.
"Like many of our fans, we believe that everyone should stand for the National Anthem," Goodell wrote.
"It is an important moment in our game. We want to honour our flag and our country, and our fans expect that of us.
"We also care deeply about our players and respect their opinions and concerns about critical social issues.
"The controversy over the Anthem is a barrier to having honest conversations and making real progress on the underlying issues. We need to move past this controversy, and we want to do that together with our players."
Goodell told owners that, following discussions with clubs and players, "we have worked to develop a plan that we will review with you at next week's League meeting".
He said the plan would include giving players an 'in-season platform' to address the issues.
"I expect and look forward to a full and open discussion of these issues when we meet next week in New York," Goodell added.
"Everyone involved in the game needs to come together on a path forward to continue to be a force for good within our communities, protect the game, and preserve our relationship with fans throughout the country. The NFL is at its best when we ourselves are unified.
"In that spirit, let's resolve that next week we will meet this challenge in a unified and positive way."
NFL team owners are due to gather in New York for the Fall League Meeting.
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