In the early 1900s, Stewart organized a pro football team in Massillon, Ohio called the Massillon Tigers. Ed, a young and ambitious editor of the city newspaper The Evening Independent, was named as the team's first coach. At this time, Massillon was involved in a rivalry with the cross-county, Canton Bulldogs. Both teams spent lavish amounts of money to bring in ringers from out of town. Prior to the 1906 season, a news story in The Plain Dealer alleged that the Bulldogs were financially broke and could not pay its players for that final game. Many Canton followers believed the story had originated in Massillon as a trick to discredit their team and make it tougher for Canton to recruit players for 1906. Since Stewart had newspaper connections, he was believed by Canton to have planted the story.
In 1906, Stewart was a figure in a betting scandal between the two clubs. The Canton Bulldogs-Massillon Tigers Betting Scandal was the first major scandal in professional football. It was more notably the first known case of professional gamblers attempting to fix a professional sport. It refers to an allegation made by a Massillon newspaper charging the Bulldogs' coach, Blondy Wallace, and Tigers end, Walter East, with conspiring to fix a two game championship series between the two clubs. When the Tigers won the second and final game of the series and were named pro football's champions, Wallace was accused of throwing the game for Canton.
However, through the Massillon Independent, Stewart charged that an actual attempt was made to bribe some of the Tiger players and that Wallace had been involved.
Stewart never stated that either the first or second Canton-Massillon game was fixed. Instead his accusation was that an attempt had been made to bribe some Massillion players before the first game. According Stewart, Tiny Maxwell and Bob Shiring of Massillon had been solicited to throw the first game by East. Maxwell and Shiring then reported the offer to Wightman and the scandal ended before it began. East was then released by the Tigers. Only then was Wallace named by Stewart of being East's accomplice.
The scandal was said to have ruined professional football in Ohio until the mid 1910s. However, some others argue that the expense of placing all-star teams on the field each week also put a damper on the sport. The Canton Morning News put a $20,000 price tag on the Massillon Tigers 1906 team, while many speculate that the Bulldogs roster probably cost even more. Stiil others contend that the games involving top teams such as Canton and Massilon were too one-sided and lacked excitement. Many towns in Ohio still fielded clubs over the next several years, however these new pros consisted more of sandlotters, with only the occasional ringer. A second incarnation of the Bulldogs would be established in 1911 and would later go on to win two championships in the National Football League.
Stewart's first collegiate head coaching position was as the head football coach at Mount Union College. He coached one season there and posted a 9–2 record. Stewart was also the head coach of the Mount Union men's basketball team for one season. He coached the team for one season posting a record of 18–3 in the 1907–08 season.
From 1911 to 1916, Stewart was the head coach of the men's basketball team at Oregon State, then known as Oregon Agricultural College. In his five seasons as the head basketball coach at OAC, Stewart posted a record of 67–33.
While at Oregon State, he also coached the Oregon State Beavers baseball team during the 1912 season. He coached the team to a 5–9 record.
Pulling the triple threat for Oregon State, Stewart also coached the Oregon State Beavers football team from 1913 to 1915. In football he compiled a 15–5–5 record.
From 1916 to 1917, Stewart was the head coach of the University of Nebraska football team. In his two seasons at the helm, he led the team to the Missouri Valley Conference title each year and posted an 11–4 record overall. After the conclusion of the 1917 football season, Stewart took over as head basketball coach and remained in that capacity from 1917 to 1919. He coached the Cornhuskers to a 17–14 record over those two seasons.
In the spring of 1921, Stewart became the head baseball coach at Clemson Agricultural College of South Carolina. That spring was a busy one for Stewart as he also coached the track and field team and ran spring practice for football, all while coaching the baseball team. He coached the baseball team for just the 1921 season and the track program from 1921 to 1923.
In the fall of 1921, Stewart coached his first season of football at Clemson. He remained there for two seasons, the 1921 and 1922 seasons, and compiled a 6–10–2 record.
As soon as the football season of 1921 ended, Stewart jumped into his 4th head coaching role at Clemson at coached the basketball team. He coached the basketball from 1921 to 1923. In his two seasons at the helm, he led Clemson to a 19–19 record.
A medical school graduate, a piano enthusiast, a former sportswriter, a one-time automobile dealership owner, and a veteran coach, E.J. Stewart quickly became a popular figure across diverse segments of the University population. His oratory eloquence landed him an open job offer from the head of the UT English Department, should he ever decide to quit coaching and desire other work.
Some have speculated that Stewart's devotion to his varied non-athletic interests was the root cause of his football and basketball teams' decline in performance over his tenure. He led the Longhorn football team to an 8–0–1 record during the 1923 season; his following teams finished with records of 5–3–1, 6–2–1, and 5–4. Stewart led the Longhorn basketball team to a perfect 23–0 mark and a Southwest Conference championship during the 1923–24 season, but his subsequent teams finished 17–8, 12–10, and 13–9.
This decline in his teams' performance resulted in the popular Stewart's controversial dismissal following the 1926–27 season.
He ended his career at University of Texas at El Paso where he compiled a 5–6–3 record. On November 18, 1929, Stewart was shot and killed by a deer-hunting companion. He was interred at Lakeview Cemetery in Cleveland.