Nebraska's football team began its history as the "Old Gold Knights", and was also sometimes known as the "Tree Planters", "Nebraskans", "The Rattlesnake Boys", "Red Stockings", "Antelopes" or "Goldenrods" in their early years.
Nebraska's high level of turnover at the top continued as yet another new head coach arrived. Coach Branch was recently finished with school, and the Nebraska appointment was his first college head coaching position.
The University met the Lincoln High School football team for the second time in this exhibition game, and came away with a 6-0 win although it did not count towards the season record. There does not seem to be a historical record to indicate that the score was the result of a close fought game or the Bugeaters not pushing as hard as they could have, though the way the season went perhaps credit is due to the high schoolers. Nebraska was now 2-0 against Lincoln High School. 
Nebraska suffered its worst ever defeat to open the official slate for 1899, falling behind at Iowa State by 28-0 at halftime. The ineffective Bugeater offense was never able to come up with anything all day, and the preparation of the Cyclones showed the value of the practices they had been getting in since August. Nebraska slipped to 2-2 all time against Iowa State. 
The first half remained scoreless as both teams fought to gain a foothold. Nebraska's defense had improved over the previous week, but only enough so that the teams were merely evenly matched. Both squads managed a second half touchdown each but could do nothing further to decide the match, fittingly leaving these squads with an evenly divided 1-1-1 all-time record, as well as one recorded cancellation from 1897. 
Nebraska's offensive woes and ineptitude continued as Missouri walked all over the Bugeaters in Lincoln. The Bugeater defense remained stout, however, keeping the scoring from getting out of hand. Without any offense, however, Nebraska suffered their second shutout loss of the season as Missouri drew closer to Nebraska in the series by pulling up to 3-5.
The Kansas City Medics brought Nebraska to their home field and proceeded to demolish the Bugeaters, settling the issue of the tied game from two weeks prior. The Medics pulled ahead on the series 2-1-1, and the Nebraska season began to spiral downhill. 
At last, after four losses and a tie to start the season (excluding the exhibition game), Nebraska finally managed to put up a 'W' on the books with a close win at Drake, getting out of Des Moines with a one-score margin of victory and evening the Drake series at 1-1. 
The 1899 Nebraska collapse finally became serious enough to warrant media attention that survives to the present day, as speculation regarding team captain Williams and his leadership swirled amongst rumors that he might quit the team. Nebraska did manage to outscore Kansas by 3 points in the second half, but coming after a 24-5 first half deficit, it was of no value. Kansas increased their series lead to 5-3. 
It may have seemed like the light was shining on Nebraska briefly, as they pulled ahead 5-0 in their first ever game against South Dakota. The Bugeaters drew as close as South Dakota's 5-yard line later on, but failed to score before the half and never put any more points up. South Dakota's 6 points in the second half brought defeat upon the Bugeaters yet again. Following this game, Captain Williams did in fact leave the program. 
The indignity of the 1899 season fittingly ended on a muddy, wet field in Omaha with Grinnell's 12-0 shutout defeat of the Bugeaters to close out what was by far the worst season in program history. Nebraska fell to 1-2 against Grinnell all time.
The disastrous 1899 season was Nebraska's first losing season. Coach Branch departed after his one and only season. His single-season record of 1-7-1 (.167) was the worst single season record in program history until 1957, and brought Nebraska's overall program record down to 41-25-4 (.614).
1899 was the first year that the nickname "Cornhuskers" was used to identify the team, used by Charles "Cy" Sherman in one of his pieces written for the Nebraska State Journal, and it was adopted as the official team name beginning next season.