On January 19, 1965, the day before the inauguration, Vice President-elect Humphrey told the Democratic National Committee that the party had unified because of the national consensus established by the presidential election.
Humphrey took office on January 20, 1965, ending the 14-month vacancy of the Vice President of the United States, which had remained empty when then-Vice President Lyndon B. Johnson assumed the Presidency after the assassination of John F. Kennedy. He was an early skeptic of the then growing Vietnam War. Following a successful Viet Cong hit-and-run attack on a US military installation at Pleiku on February 7, 1965 (where 7 Americans were killed and 109 wounded), Humphrey returned from Georgia to Washington D.C., to attempt to prevent further escalation. He told President Johnson that bombing North Vietnam was not a solution to the problems in South Vietnam, but that bombing would require the injection of US ground forces into South Vietnam to protect the airbases. Presciently, he noted that a military solution in Vietnam would take several years, well beyond the next election cycle. In response to this advice, President Johnson punished Humphrey by treating him coldly and restricting him from his inner circle for a number of months, until Humphrey decided to "get back on the team" and fully support the war effort.
On April 15, 1965, Humphrey delivered an address to the American Society of Newspaper Editors, pledging the incumbent session of Congress would "do more for the lasting long-term health of this nation" since the initial session in office at the time of Franklin D. Roosevelt assuming the presidency in 1933 and predicting 13 major measures of President Johnson's administration would be passed ahead of the session's conclusion. In mid-May 1965, Humphrey traveled to Dallas, Texas for an off-the-record discussion with donors of President Johnson's campaign. During the visit, Humphrey was imposed tight security as a result of the JFK assassination a year and a half prior and the mother of Lee Harvey Oswald was placed under surveillance by Police Chief Cato Hightower.
In February 1965, President Johnson appointed Humphrey to the chairmanship of the President's Council on Equal Opportunity. The position and board had been proposed by Humphrey, who told Johnson that the board should consist of members of the Cabinet and federal agency leaders and serve multiple roles: assisting agency cooperation, creating federal program consistency, using advanced planning to avoid potential racial unrest, creating public policy, and meeting with local and state level leaders. During his tenure, he appointed Wiley A. Branton as executive director. During the first meeting of the group on March 3, Humphrey stated the budget was US$289,000 and pledged to ensure vigorous work by the small staff. Following the Watts riots in August of that year, Johnson downsized Humphrey's role as the administration's expert on civil rights. Dallek wrote the shift in role was in line with the change in policy the Johnson administration underwent in response to "the changing political mood in the country on aid to African Americans." In a private meeting with Joseph Califano on September 18, 1965, President Johnson stated his intent to remove Humphrey from the post of "point man" on civil rights within the administration, believing the vice president was tasked with enough work. Days later, Humphrey met with Johnson, Attorney General Nicholas Katzenbach, and White House Counsel Lee C. White. Johnson told Humphrey he would shorten his role within the administration's civil rights policies and pass a portion to Katzenbach, Califano writing that Humphrey agreed to go along with the plan reluctantly.
December 1965 saw the beginning of Humphrey's tour of eastern countries, saying he hoped to have "cordial and frank discussions" ahead of the trip beginning when asked about the content of the talks. During a December 29 meeting with Prime Minister of Japan Eisaku Satō, Humphrey asked the latter for support on achieving peace in the Vietnam War and said it was a showing of strength that the United States wanted a peaceful ending rather than a display of weakness.
In 1965, Humphrey was made an Honorary Life Member of Alpha Phi Alpha, a historically African American fraternity.