After leaving Cornell the first time, Warner became head coach of the football team at Carlisle Indian Industrial School in 1899, a flagship Indian boarding school founded to teach children and young men skills to advance in American society.
Its late-nineteenth- and early-twentieth-century football teams were nationally prominent, and Warner was paid $1,200 (approximately $33,000 in 2016), an exceptionally high salary for a coach at the time.

His previous Cornell team once faced Carlisle, and he was impressed by his opponent's approach to the game.
Since the players were outweighed by every other team in the nation, they relied on speed and agility instead of size and physical force.
Despite those strengths, Cornell won the game 23 to 6.
The referee was a former Cornell graduate and was accused of helping out Cornell during the game.
After the match, and in addressing the journalists, Warner acknowledged that there was assistance from the referee.
He stated  that "We outscored 'em but we didn't defeat 'em, if you follow me."
It has been said that after that game he considered Carlisle to be the future of college football.

The head coach dealt with young players who differed from the white, East-Coast students with whom he had previously worked.
At the beginning, he used the then-customary coaching methods of rough language and a strict routine.
The Native American students were unaccustomed to such an approach, and several key players stopped attending practices.
Warner adjusted his technique, saying that he "found I could get better results.
I don't think I ever swore at a player from that time.
Maybe I did a little cussing, now and then, but never at players."

His coaching brought immediate improvement.
In 1897 and 1898, the Carlisle teams had 6–4 records.
In 1899 (Warner's first year), Carlisle won nine and lost two games—to the country's two best teams: Harvard and Princeton.
That year saw Carlisle's first major victory, against one of the "Big Four" teams, beating Penn 16–5.
At the end of the season, the school played Columbia at the Polo Grounds in New York City, a premier sports venue at the time, defeating them 42–0.
The Columbia game was the first time that a crouching start, a form of what is now known as a three point stance, was used by the running backs.
Before Warner's innovation, the stance for a back before the ball was snapped was bent forward with his feet well apart and his hands on his knees.
Warner realized that if his players took a stance similar to the one taken by sprinters, the legs would be bent, the back leaning forward, with one hand on the ground and the other arm cocked back to the thigh/hip region.
Like with sprinters, this similar stance maximized the speed of his players.
Shortly after, it became the standard football stance for both backs and linemen.

At the end of 1899, Warner was appointed the school's athletic director and his salary more than doubled.
A track-and-field program was started that year.
Warner knew little about the sport; to prepare as coach he bought every book available and consulted Jack Moakley and Mike Murphy, two of the era's leading head coaches.
The program was successful; running was a Native American tradition, and students from the Southwest were known for their stamina in long-distance races.

Warner's next two years were less fruitful.
The 1900 football team went 6–4–1, losing three games to the Big Four, and the 1901 season was a losing one, with Carlisle posting a 5–7–1 record.
The following year, the team posted an improved 8–3 record, when Warner began implementing double (lateral) passes.
Carlisle's quarterback Jimmy Johnson would make a lateral pass to the halfback running towards the sideline, bringing the defense with him as he tossed the ball back to the fast-running Johnson.

In 1902, Warner played one professional football game for the Syracuse Athletic Club during the first World Series of Football at Madison Square Garden.
In the first professional indoor football game, Syracuse defeated the heavily favored New York team.
During the series, Warn
After leaving Cornell the first time, Warner became head coach of the football team at Carlisle Indian Industrial School in 1899, a flagship Indian boarding school founded to teach children and young men skills to advance in American society. Its late-nineteenth- and early-twentieth-century football teams were nationally prominent, and Warner was paid $1,200 (approximately $33,000 in 2016), an exceptionally high salary for a coach at the time.
His previous Cornell team once faced Carlisle, and he was impressed by his opponent's approach to the game. Since the players were outweighed by every other team in the nation, they relied on speed and agility instead of size and physical force. Despite those strengths, Cornell won the game 23 to 6. The referee was a former Cornell graduate and was accused of helping out Cornell during the game. After the match, and in addressing the journalists, Warner acknowledged that there was assistance from the referee. He stated  that "We outscored 'em but we didn't defeat 'em, if you follow me." It has been said that after that game he considered Carlisle to be the future of college football.
The head coach dealt with young players who differed from the white, East-Coast students with whom he had previously worked. At the beginning, he used the then-customary coaching methods of rough language and a strict routine. The Native American students were unaccustomed to such an approach, and several key players stopped attending practices. Warner adjusted his technique, saying that he "found I could get better results. I don't think I ever swore at a player from that time. Maybe I did a little cussing, now and then, but never at players."
His coaching brought immediate improvement. In 1897 and 1898, the Carlisle teams had 6–4 records. In 1899 (Warner's first year), Carlisle won nine and lost two games—to the country's two best teams: Harvard and Princeton. That year saw Carlisle's first major victory, against one of the "Big Four" teams, beating Penn 16–5. At the end of the season, the school played Columbia at the Polo Grounds in New York City, a premier sports venue at the time, defeating them 42–0. The Columbia game was the first time that a crouching start, a form of what is now known as a three point stance, was used by the running backs. Before Warner's innovation, the stance for a back before the ball was snapped was bent forward with his feet well apart and his hands on his knees. Warner realized that if his players took a stance similar to the one taken by sprinters, the legs would be bent, the back leaning forward, with one hand on the ground and the other arm cocked back to the thigh/hip region. Like with sprinters, this similar stance maximized the speed of his players. Shortly after, it became the standard football stance for both backs and linemen.
At the end of 1899, Warner was appointed the school's athletic director and his salary more than doubled. A track-and-field program was started that year. Warner knew little about the sport; to prepare as coach he bought every book available and consulted Jack Moakley and Mike Murphy, two of the era's leading head coaches. The program was successful; running was a Native American tradition, and students from the Southwest were known for their stamina in long-distance races.
Warner's next two years were less fruitful. The 1900 football team went 6–4–1, losing three games to the Big Four, and the 1901 season was a losing one, with Carlisle posting a 5–7–1 record. The following year, the team posted an improved 8–3 record, when Warner began implementing double (lateral) passes. Carlisle's quarterback Jimmy Johnson would make a lateral pass to the halfback running towards the sideline, bringing the defense with him as he tossed the ball back to the fast-running Johnson.
In 1902, Warner played one professional football game for the Syracuse Athletic Club during the first World Series of Football at Madison Square Garden. In the first professional indoor football game, Syracuse defeated the heavily favored New York team. During the series, Warn
Pop Warner