Rote attended Rice University from 1946–49, quarterbacking the Owls under the leadership of head coach Jess Neely. As a senior in 1949, Rote led the Owls to a 10–1 season, capped by a 27–13 win over North Carolina in the Cotton Bowl. During the fourth game of the season against rival Southern Methodist that featured cousin Kyle Rote, he led the Owls back from a 14–0 deficit to a 41–27 win. The next week saw Rote lead a comeback against Texas, turning a 9–0 halftime deficit into a 17–15 win. With a flawless conference record, the Owls were named outright Southwest Conference champions for the third time.
The Green Bay Packers selected Rote in the second round (17th overall) of the 1950 NFL Draft. He would spend a total of seven seasons in Wisconsin, leading the hapless Packers' offense while the defense annually ranked among the league's worst. Besides his passing duties, Rote led the Packers in rushing yards three times and rushing touchdowns five times. During the span of his Green Bay career, Rote ranked third in the NFL in passing touchdowns, trailing only Bobby Layne and Norm Van Brocklin. He also ranked first in the league in rushing yards by a quarterback and second in touchdowns.
Rote's 1956 season ranks among the greatest in NFL history. On a 4–8 team, he led the league in passing yards (by 294), passing touchdowns (his 18 being six more than Ted Marchibroda's 12). In addition, his 11 rushing touchdowns were second in the league behind only those of Chicago'sRick Casares. His 29 total touchdowns were the highest single-season total in NFL history to date and the highest total in the era of the twelve-game schedule. The entire Packers' offense outside of Rote accounted for just 5 touchdowns.
Among quarterbacks, he led the league in pass completions, pass attempts, passing yards, passing touchdowns, rushing attempts, rushing yards, and rushing touchdowns.
Rote split time with Bobby Layne, although it was Rote who ended up with more passing touchdowns, fewer interceptions, more rushing yards, more rushing touchdowns, and a better won-lost record as a starter. Layne broke his leg late in the year, leaving Rote to guide the team to an NFL title. Detroit tied San Francisco for the division title, forcing a one-game playoff. Facing a 27–7 deficit in the third quarter, Rote led the Lions to a 31–27 comeback win and a date with the Cleveland Browns. In one of the greatest playoff performances in history, Rote led the Lions to a 59–14 thumping of the Browns. He completed 12 of 19 passes for 280 yards and 4 touchdowns, adding another touchdown on the ground.
As for Green Bay, they averaged four points/game fewer than the year before in spite of the addition of future Hall of Famers Bart Starr and Paul Hornung.
Layne was traded to Pittsburgh shortly into the 1958 season, leaving Rote to guide the aging and rapidly declining Lions. Rote would lead the team in rushing, making it the fourth time in his career that he did so (an NFL record for quarterbacks). After a disastrous 1959 season, the Lions informed Rote that he would be released. Rather than retire, he headed north of the border to the Toronto Argonauts of the CFL.
His three seasons with the Toronto Argonauts were quite eventful. He completed 662 of 1187 passes for 9,872 yards and 62 TDs. His 38 TD passes in 1960 was an all-time CFL record. In Rote's first season with the Argos he became the CFL's second quarterback to exceed 4,000 yards passing in a season with 4,247. He also threw 38 touchdowns that season which was then a league record. Thanks to Rote's leadership the 10–4–0 Argonauts in 1960 accomplished something they had not done since 1937: finish in first place. However they lost the conference final series to Ottawa Rough Riders who went on to win the Grey Cup. Rote's 108 yard pass to Jim Rountree in 1961 is still a team record, and in 1960 he threw seven touchdown passes in a game twice, this being a CFL record at the time.
Looking for a quarterback to lead the team while a young John Hadl developed, the San Diego Chargers of the American Football League came calling. Rote was 35 years old at the time, but led the Chargers to an 11–3 record. For his part in directing the league's top offense, Rote was named first-team All-AFL and captured the Associated Press Player of the Year award. Proving that his 1957 performance was no fluke, he led the Chargers to a 51–10 win over the Boston Patriots in the championship game. Individually, he accounted for 173 yards and 2 touchdowns on 10/15 passing, plus another 15 rushing yards and a touchdown on the ground.
In 1964, Hadl began receiving more playing time. The Chargers went from 11–3 to 8–5–1 and the offense fell from first in the AFL to fourthth. Rote was the starter for the 1964 AFL Championship game against the Buffalo Bills, but neither he nor Hadl could do much against the swarming defense. Buffalo won 20–7, and Rote announced his retirement.