Goodell, along with several owners and at least two other NFL executives, will be asked to turn over all cell phone records and emails in the pending case brought forward by the former San Francisco 49ers quarterback, a league source told ESPN's Adam Schefter.
Other league executives who will be deposed include executive vice president/football operations Troy Vincent and senior vice president of player engagement Arthur McAfee, according to Sunday's ESPN report.
Kaepernick filed a grievance under the collective bargaining agreement against the NFL last month, accusing all 32 owners of collusion against signing him to an NFL contract.
Kaepernick, who turned 30 on Friday, previously said his agent reached out to all NFL teams to make sure they were aware of his interest in playing this season. He opted out of his contract with the 49ers in March and remains unsigned.
Goodell has stated on multiple occasions this season that Kaepernick is not being blackballed.
Kaepernick has been a controversial figure since he first sat and then knelt during the national anthem before games with the 49ers in the 2016 season as a protest to denounce police brutality against African-Americans, social injustice and racial inequality.
NFL owners and executives have been scrambling in recent weeks to determine the best response to players kneeling during the national anthem this season.
A number of players followed Kaepernick's lead by taking a knee during the anthem last year and this season. The movement turned into league-wide protests earlier this season after President Donald Trump made multiple critical comments of players who don't stand for the national anthem.
NFL players who have demonstrated during the national anthem have said they are protesting racial inequality, but not the flag or the anthem itself.
Kaepernick did not go through the NFL Players Association with his collusion case, instead hiring Mark Geragos, who has represented a number of high-profile clients including Michael Jackson and musician Chris Brown.
After filing the grievance, Kaepernick tweeted he filed "only after pursuing every possible avenue with all NFL teams and their executives."