Kaepernick has been out of the NFL since the end of the 2016 season, during which the quarterback attracted controversy by kneeling for the United States national anthem in protest against racial injustice and police brutality.
He filed a grievance against the NFL in 2017, accusing owners of colluding to keep him out of a job. Kaepernick settled that grievance in February.
The 32-year-old, who was involved in an NFL workout in November last year, and his protests have received renewed attention amid nationwide protests after the death of George Floyd in police custody on May 25.
Asked about Kaepernick and his future, Goodell told ESPN on Monday: "Well, listen, if he wants to resume his career in the NFL, then obviously it's gonna take a team to make that decision. But I welcome that, support a club making that decision and encourage them to do that.
"If his efforts are not on the field but continuing to work in this space, we welcome him to that table and to help us, guide us, help us make better decisions about the kinds of things that need to be done in the communities.
"We have invited him in before, and we want to make sure that everybody's welcome at that table and trying to help us deal with some very complex, difficult issues that have been around for a long time.
"But I hope we're at a point now where everybody's committed to making long-term, sustainable change."
On Kaepernick's protests in 2016, Goodell added: "What they were talking about and what they were protesting and what they were trying to bring attention to was playing out right in front of us -- and tragically.
"And so all of us saw that, and it was difficult for all of us. And so that was an important point for all of us."