On March 28, 2018, President Donald Trump announced his intent to nominate Jackson to serve as his secretary of veterans affairs. Trump wrote in a tweet, "I am pleased to announce that I intend to nominate highly respected Admiral Ronny L. Jackson, MD, as the new Secretary of Veterans Affairs. In the interim, Hon. Robert Wilkie of DOD will serve as Acting Secretary. I am thankful for Dr. David Shulkin’s service to our country and to our GREAT VETERANS!" Jackson was formally nominated to the position on April 16, 2018. On April 24, 2018, the Senate Committee on Veterans' Affairs postponed a confirmation hearing for Jackson. Sens. Johnny Isakson (R-Ga.) and Jon Tester (D-Mont.), chairman and ranking member of the Senate Committee on Veterans’ Affairs, released the following statement regarding the decision: “The Senate Committee on Veterans’ Affairs is postponing the hearing to consider the nominee to be secretary of the U.S. Department of Veterans Affairs in light of new information presented to the committee. We take very seriously our constitutional duty to thoroughly and carefully vet each nominee sent to the Senate for confirmation. We will continue looking into these serious allegations and have requested additional information from the White House to enable the committee to conduct a full review.” According to CBS News, Tester's staff was "reviewing multiple allegations of a 'hostile work environment.' The accusations include 'excessive drinking on the job, improperly dispensing meds,' said one of the people familiar, who was granted anonymity to speak frankly about the situation." Jackson said that the allegations were false and that he was "looking forward to the hearing, so we can sit down and I can explain everything to everyone and answer all the senators’ questions." When asked about the allegations, President Donald Trump said that it was up to Jackson if he wanted to withdraw his nomination. He said, “It’s totally his decision, he’ll be making a decision." Trump said that he told Jackson, “This is a vicious group of people that malign. What do you need this for? … You’re too fine a person.” The White House also released a statement supporting Jackson. White House spokesman Hogan Gidley said, "Admiral Jackson’s record of strong, decisive leadership is exactly what’s needed at the VA to ensure our veterans receive the benefits they deserve." Jackson was initially scheduled to appear before the committee on April 25, 2018. On April 26, 2018, Jackson withdrew his nomination. In a statement, he said, "While I will forever be grateful for the trust and confidence President Trump has placed in me by giving me this opportunity, I am regretfully withdrawing my nomination to be Secretary for the Department of Veterans Affairs. The allegations against me are completely false and fabricated. If they had any merit, I would not have been selected, promoted and entrusted to serve in such a sensitive and important role as physician to three presidents over the past 12 years. ... Unfortunately, because of how Washington works, these false allegations have become a distraction for this president and the important issue we must be addressing — how we give the best care to our nation’s heroes."

Congress convened a joint session on January 6-7, 2021, to count electoral votes by state and confirm the results of the 2020 presidential election. Jackson voted against certifying the electoral votes from Arizona and Pennsylvania. The House rejected both objections by a vote of 121-303 for Arizona and 138-282 for Pennsylvania.