Alan S. Boyd, the first United States secretary of transportation, who was named by President Lyndon B. Johnson in 1966 to integrate the nation’s sprawling networks of planes, trains, ships and highways into a new superagency, died on Sunday in Seattle. He was 98.

He died at Aegis at Ravenna, a retirement home, his son Mark Boyd said.

Despite resistance from bureaucrats and maritime unions, and having to work with underfunded mass transit systems, Mr. Boyd won relatively high marks for a two-year effort to merge dozens of transportation-related federal agencies into a cabinet-level department with 95,000 employees and a more than $5 billion budget. The main holdout was the Maritime Administration, which was not brought into the fold until 1981.

A half-century after Mr. Boyd laid the foundations, the Department of Transportation’s $76.5 billion budget and 54,700 employees regulate aviation, railroads, mass transit, shipping, highways, pipelines, the St. Lawrence Seaway and other transport entities. After the Sept. 11 attacks, the Transportation Security Administration and the Coast Guard were transferred in 2003 to a new Department of Homeland Security.

It was perhaps inevitable that Mr. Boyd would find a life in transportation. A great-grandfather invented America’s first horse-drawn streetcar on rails, his father was a highway engineer, and his stepfather was a lawyer for a railroad company. At 17, Alan visited the 1939 World’s Fair in New York City and was dazzled by a General Motors exhibit: a futuristic diorama of superhighways crisscrossing the country.

In Washington for nearly a decade, Mr. Boyd was a member of the Civil Aeronautics Board under President Dwight D. Eisenhower and its chairman under President John F. Kennedy. In the Johnson administration, he was the under secretary of commerce for transportation, and then the secretary of transportation from Jan. 16, 1967, to the start of the Nixon administration on Jan. 20, 1969.

After his time at the transportation department, he took on a number of private and public roles. He was president of the Illinois Central Railroad; President Jimmy Carter’s chief negotiator for a 1977 air-travel pact with Britain, called Bermuda II, governing fares, air routes and other trans-Atlantic arrangements; president of Amtrak; and finally president of the North American arm of Airbus Industrie, the French jetliner manufacturer.

While Mr. Boyd’s succession of titles and associations with presidents made an impressive record, his success was hardly a smooth upward trajectory; rather, it was a series of disjointed, sometimes chance events, as he recalled in an autobiography, “A Great Honor: My Life Shaping 20th Century Transportation” (2016). (His eyesight failing at 93, Mr. Boyd dictated the book into a recorder, and completed it with the assistance of his son.)

Mr. Boyd flunked out of college, but eventually returned and went on to become a lawyer and to receive four honorary doctorates. He was hit by lightning after enlisting in the military and was saved by CPR, but hid the incident from medics to qualify for the Army Air Forces. He became a World War II C-47 pilot, ferrying paratroops into Normandy on D-Day and supplies to besieged Americans at the Battle of the Bulge. After the war, he was rejected for an entry-level job with the Civil Aeronautics Board, but a decade later became the board’s chairman.

It was happenstance that brought Mr. Boyd to the attention of Johnson, in 1961, when Johnson was vice president, leading to a lasting bond and Mr. Boyd’s rise to prominence in Washington. Johnson’s private plane had crashed en route to pick him up at his Texas ranch, and both pilots had been killed. It was Mr. Boyd’s turn in a rotation at the Civil Aeronautics Board, which regulated the airline industry, to lead the accident investigation. Johnson did not forget him or his thorough work.

In 1965, as president, Johnson named Mr. Boyd under secretary of commerce for transportation. Mr. Boyd soon resolved to end what he regarded as wasteful federal subsidies to American merchant ships. Invited to the Oval Office to discuss his plan with Johnson and his chief domestic aide, Joseph A. Califano Jr., Mr. Boyd, according to his memoir, got into a heated dispute with the president:

“‘You don’t know what you’re talking about, Alan,’ Johnson said. ‘The merchant marine is our fourth arm of defense. If we got into another war without it, we would be totally helpless.’

“‘Mr. President,’ I said, ‘you are crazy as hell.’

“Joe seemed shocked that I would address the president in such a tone. But I had gotten to know the president, and knew he would take my comments in stride. I pointed out that American shipping companies owned hundreds of ships registered under flags of convenience. Those ships had served the United States during World War II and Korea, and they would be available in case of future need.

“ ‘All right, you bastard,’ the president shot back. ‘I know you’re right. And I also know you’re going to get us both killed politically. I’ll support you for a year. See what you can do.’”

Mr. Boyd used the year. He made his case to shipowners, the Seafarers International Union and to Congress, but got nowhere. The subsidies were too entrenched. He told the president he had failed.

“I knew you would, Alan,” Johnson had said, according to Mr. Boyd’s memoir. “But you gave it a good try.”

In 1966, Johnson revived a long-discussed idea of streamlining the nation’s fragmented transportation systems. There were 35 agencies with related responsibilities. Americans spent 20 percent of their income on transportation. Mr. Boyd led a group that studied the problems, wrote a bill to create the Department of Transportation and shepherded it through Congress.

Johnson signed the bill into law on Oct. 15, 1966, and the department began operation on April 1, 1967. Mr. Boyd, confirmed by the Senate without opposition as the first transportation secretary, picked both Democrats and Republicans as aides, insisting that transportation was nonpartisan. He plunged into airport modernization, air traffic control improvements, enforcement of auto safety standards and driver education.

But congressional appropriations dictated that 80 percent of his budget be earmarked for highways, including for Lady Bird Johnson’s highway beautification program, while airlines, railroads and mass transit got short shrift. “We’ve got a bucketful of money for highways and only a medicine dropperful for the rest,” Mr. Boyd told Forbes magazine in 1968. He said his hands were tied.

He also found that unifying many agencies was a thicket. “No matter what you wanted to do or what change you suggested, the response was classically, ‘That’s not the way we do it here,’” he wrote in his memoir.

Shipowners and maritime unions never forgot Mr. Boyd’s opposition to their subsidies, and it took 15 years to incorporate the Maritime Administration into the department.

When it was introduced in 1981, the supersonic transport plane seemed to represent the future of passenger air travel, but studies called it costly, inefficient and noisy. British and French versions were built, but Congress ended funding for the plane.

When Richard M. Nixon was elected president in 1968, Mr. Boyd, looking for a new job, considered a run for the Senate, but moved to Chicago and became president and chief executive of the Illinois Central Railroad from 1969 to 1972. He was accused of a conflict of interest because the railroad had just received a $25 million grant from the federal Transportation Department. But an inquiry found that he had had no role in making the grant.

As president of Amtrak, the government-supported National Railroad Passenger Corporation, from 1978 to 1982, Mr. Boyd fought cutbacks in funding and service. But subsidies dwindled. When he left, he said his chief regret was failing to establish permanent funding for Amtrak. With Airbus, from 1982 to 1992, his biggest sale was to Braniff Airlines in 1989, a $3.5 billion deal for 100 planes.

Alan Stephenson Boyd was born in Jacksonville, Fla., on July 20, 1922, to Clarence and Elizabeth (Stephenson) Boyd. His maternal great-grandfather, John Stephenson, had patented the first streetcar on rails in America, a horse-drawn coach that began operations in Manhattan in 1832.

Clarence Boyd, an engineer for the Florida Highway Department, died when Alan was 2. Ms. Boyd, Alan and his sister, Jean, lived with aunts and uncles until their mother married Walter Dopson, a lawyer for Seaboard Air Line Railroad.

Alan graduated from Macclenny-Glen High School (now Baker County High School) in northeast Florida in 1939. He enrolled at the University of Florida but flunked out at the end of his second year. He joined the Army Air Forces after the United States had entered World War II.

In 1943, he married Flavil Townsend, a high school teacher. They had one son, Mark. Mr. Boyd’s wife died in 2007. Besides his son, he is survived by two grandchildren and one great-grandchild.

Mr. Boyd earned a law degree at the University of Virginia in 1948. He joined a Miami law firm whose senior partner was George A. Smathers, a two-term Democratic congressman who won a United States Senate seat in 1950. Mr. Boyd worked on the Smathers campaign.

A decade later, after he had become general counsel for the Florida State Turnpike Authority and chairman of the Florida Railroad and Public Utilities Commission, Mr. Boyd received a call from Senator Smathers in Washington. There was a vacancy on the Civil Aeronautics Board. Was he interested? He soon began his years in Washington.

Mr. Boyd, who retired in 1993, returned to Washington in 2017 for a celebration of the 50th anniversary of the Department of Transportation. He told a crowd of 500 dignitaries that soon after taking office in 1967, he had received a call from Henry Ford II, chief executive of Ford Motor at the time, who told him that American motorists didn’t want and would never use safety belts in their cars.

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