Over the course of the season, Frank Thomas was riddled with health issues that ultimately led to his resignation as head coach. In January 1947, Harold Drew was named as the 17th head coach of the Crimson Tide.
To open the 1946 season, the Crimson Tide played the FurmanPurple Hurricane, who fielded their first team since the 1942 season, on a Friday night at Legion Field. Against the Purple Hurricane, Alabama won 26–7 before a crowd of 25,000 in Birmingham. In the first quarter, Alabama took a 6–0 lead after Norwood Hodges intercepted a Skeeter Coyle pass and returned it 27-yards for a touchdown. On the kickoff that ensued, Charlie Truluck returned it 95-yards to give Furman a 7–6 lead. The Crimson Tide responded with a pair of second-quarter touchdowns to take a 19–7 halftime lead. The first came on a 29-yard Harry Gilmer pass to Ted Cook and the second on a six-yard Johnny August run. Alabama then scored their final points of the game in the third quarter on a 15-yard Gilmer run. The victory improved Alabama's all-time record against Furman to 2–0.
To open conference play, Alabama traveled to New Orleans and defeated the TulaneGreen Wave 7–6 in what was described as a "torrential downpour" throughout the game. Alabama scored their only points on a two-yard Hal Self touchdown run in the first quarter, and Tulane scored on a 24-yard Jim Keeton pass to John Sims in the second quarter. At the time, the announced crowd of 64,317 in attendance for the game was the largest for a regular season game in the Southern United States. The victory improved Alabama's all-time record against Tulane to 15–4–1.
Against the South CarolinaGamecocks, Alabama won their third game of the season with this 14–6 at Carolina Stadium. The Gamecocks took a 6–0 first quarter lead after Bo Hagan threw a 42-yard touchdown pass to Earl Dunham. Alabama responded with a one-yard Hal Smith touchdown run for a 7–6 halftime lead. After a scoreless third, the Crimson Tide closed the game with a one-yard Fred Grant touchdown run for the 14–6 win. The victory improved Alabama's all-time record against South Carolina to 4–0.
After they opened the season with three consecutive victories, Alabama was recognized with the No. 6 ranking in the first AP Poll for the 1946 season in the week that led to their game against the Southwestern Louisiana Institute. Against the Bulldogs, that were led by former Tide great Johnny Cain, Alabama won their fourth game of the season with their 54–0 shutout at Denny Stadium. Alabama took a 6–0 first-quarter lead after Lowell Tew scored on a 28-yard touchdown run. They extended their lead 20–0 at halftime after Johnny August threw a 15-yard touchdown pass to Bob Hood and Lionel W. Noonan scored on a three-yard run.
In the third quarter, Tew scored his second touchdown on a seven-yard run and Fred Grant scored on a three-yard run for a 34–0 lead. The Crimson Tide then concluded the afternoon with a trio of touchdowns in the fourth quarter. The touchdowns were scored on a Clem Welsh run, a 46-yard Norman Mosley punt return and an 87-yard D. Joe Gambrell reception from Theo Fakier for the 54–0 victory. The victory improved Alabama's all-time record against the Bulldogs to 3–0.
Although they defeated Southwestern Louisiana in their previous game, Alabama dropped to the No. 7 position in the second AP Poll of the season. Against Tennessee, the Crimson Tide were shutout Volunteers 12–0 at Shields–Watkins Field. The Tennessee points were scored on short Bob Lund touchdown runs in the second and third quarters. The loss brought Alabama's all-time record against Tennessee to 16–9–3.
After their loss against Tennessee, Alabama dropped four spots to the No. 11 ranking prior to their game against Kentucky. In Montgomery, the Crimson Tide defeated the Wildcats 21–7 at the Cramton Bowl. After a scoreless first quarter, Alabama took a 14–0 halftime lead after touchdowns were scored on a one-yard Harry Gilmer run and on a 37-yard Gilmer pass to Hugh Morrow in the second quarter. Kentucky responded in the third with their only points when Bill Chambers intercepted a Gilmer pass and returned it 65-yards for a touchdown. The Crimson Tide then made the final score 21–7 in the fourth on an eight-yard Gilmer pass to Ted Cook. The victory improved Alabama's all-time record against Kentucky 23–1–1.
Although the Crimson Tide defeated Kentucky the previous week, Alabama dropped four spots to the No. 15 ranking for their game against Georgia. Against the Bulldogs, the Crimson Tide were shutout 14–0 before 30,000 fans at Sanford Stadium. Georgia All-American halfback Charley Trippi was responsible for both of the Bulldogs' touchdowns. The first came on a nine-yard Trippi pass to Dan Edwards and later on a 46-yard Trippi run. The loss brought Alabama's all-time record against Georgia to 15–14–3.
To open conference play for the 1945 season, the Crimson Tide traveled to play LSU and left Baton Rouge with a 26–7 victory. The loss brought Alabama's all-time record against LSU to 12–4–3.
Against the VanderbiltCommodores, Alabama won 12–7 at Legion Field in Birmingham. After a scoreless first quarter, the Crimson Tide took a 12–0 halftime lead after touchdowns were scored in the second quarter on a short Hal Self run and a 20-yard Harry Gilmer pass to Hugh Morrow. The Commodores scored their lone touchdown late in the fourth quarter on a one-yard Robert Berry touchdown run on fourth-and-goal to make the final score 12–7. The victory improved Alabama's all-time record against Vanderbilt to 16–10.
Against the Boston CollegeEagles, Alabama lost 13–7 in what was the first game ever played by the Crimson Tide in New England. After a scoreless first quarter, each team scored second-quarter touchdowns. The Eagles scored first on a one-yard James Benedetto run and Alabama responded with a 38-yard Harry Gilmer pass to Ted Cook to make the halftime score 7–7. Boston then scored the game-winning touchdown early in the final period on a 39-yard Maurice Poissant run. The loss brought Alabama's all-time record against Boston College to 1–1. In addition to being their first game played in New England, this game also marked the first time that an Alabama squad traveled to an away game by way of airplane.
On what was both homecoming and the final game of the season at Denny Stadium, Alabama upset the Mississippi StateMaroons 24–7. After a scoreless first quarter, Alabama took a 10–0 halftime lead after a six-yard Hugh Morrow field goal and a two-yard Lionel W. Noonan touchdown run in the second quarter. They extended their lead further to 17–0 in the third after John Wozniak returned a blocked punt 38-yards for a touchdown. The game then concluded with a pair of fourth-quarter touchdowns. The first was scored by Alabama on a one-yard Harry Gilmer run and the second for State on a short Wallace Matulich run. The victory improved Alabama's all-time record against Mississippi State to 23–7–2.
The struggles of the 1946 team might have been caused in part by the deteriorating health of coach Frank Thomas. High blood pressure left him bedridden for most of the 1946 season, unable to stand for long periods, and forced to ride in a trailer to conduct many Alabama practices. After the 1946 season his ill health forced his resignation when he was only 48 years old, and Thomas later died in Tuscaloosa on May 10, 1954. During his fifteen seasons as head coach at Alabama, Thomas won four SEC championships and compiled an overall record of 115 wins, 24 losses and seven ties (115–24–7) record, for an .812 winning percentage.
Prior to the conclusion of the season, speculation began as to who would succeed Thomas as the head coach of the Crimson Tide. In early November, sources indicated that former Thomas player, and then head coach at Kentucky, Bear Bryant was to become the next head coach of the Crimson Tide. On November 11, Bryant stated that he had not been in contact about the Alabama job and indicated his focus was on the Wildcats. After an exhaustive search, on January 14, 1947, former Thomas assistant and then head coach at Ole Miss, Harold Drew was introduced as the new head coach of the Crimson Tide.