Following the departure of Fielding H. Yost following the 1898 season, Nebraska hired Branch, a recent graduate of Williams College with little football coaching experience. In his only season as head coach, Branch led Nebraska to its first losing season, and only sub-.500 record in its first 38 years of football.
This was NU's final season as the "Bugeaters", as the university officially changed its nickname to "Cornhuskers" in 1900.
Nebraska met the Lincoln High School football team in a pre-season exhibition game for the second time. It is unclear whether the score was the result of a tightly contested game, or an act of sportsmanship by the university team against high schoolers.[5][6]
Nebraska suffered its worst-ever defeat to open the 1899 season, trailing 28–0 at halftime and losing 33–0. Iowa State had begun preparation for the football season prior to that start of the school year, a practice not commonplace at the time.[5]
After allowing 33 points to Iowa State the week prior, Nebraska's defense held the Kansas City Medics off the scoreboard in a scoreless first half. A second-half touchdown from each team culminated in a 6–6 tie.[5]
Nebraska defeated Drake 12–6 in what would be the first and only college football head coaching win for Branch (after a brief stint at Miami (OH), he ended his career with a record of 1–11–1).[5]
Despite a strong second-half performance against Kansas in Lincoln, Nebraska was unable to overcome a 24–5 deficit. The team's performance was so poor that rumors began to spread suggesting team captain and starting halfback Charles Williams may quit the team.[5]
Nebraska led 5–0 in its first-ever game against South Dakota, but were unable to capitalize on scoring opportunities in the first half. A second-half touchdown gave South Dakota a 6–5 victory. Team captain Charles Williams left the NU program following the game.[5]