For the next fourteen months following Burleson's departure, the operation of Baylor University was guided by John C. Lattimore, professor of mathematics and pedagogy, who was given the title of Chairman of the Faculty. Many thought he would eventually be named president, but in August 1899 the trustees decided on another individual. Upset with the decision, Lattimore left to become superintendent of the Waco schools.
The trustees had sought for a "scholar rich in saving common sense and ripe in young manhood; a man of Godly piety; a man of executive ability capable of not only doing much himself but of getting work out of others; a man who could appreciate his fellow workman; a man who could bring the institution favorably before the public through his own speech or writing, and furnish similar opportunities to others connected with it; a man who could unite the faculty and bring the student body in close touch with himself; a man of business sense, but of much more university sense."
Other qualifications they desired was for "a man who could give his entire time and attention to the institution and not to the holding of his job; a man not overcome by details but quick and careful, courteous and firm in the dispatch of business; a man who would not regard himself too busy to attend to the institution's affairs while shoveling the snow off his own sidewalk." The man whom they felt best fulfilled these requirements was Oscar Henry Cooper.
An 1872 graduate of Yale University at age twenty, Cooper's first job was the presidency of Henderson Male and Female College. In 1881 Cooper returned to Yale to teach. Three years later, he came back to Texas to serve as principal of Houston's high school. From 1886-1890 he was Texas' Superintendent of Public Instruction, after which he became superintendent of the Galveston public school system, the position that he held when named president of Baylor.
Cooper's presidency, though lasting just a few months short of three years, was fairly productive . His most notable achievements probably were the securing of increased recognition of Baylor's degrees by the prestigious "Eastern" universities and the acquiring from F. L. Carroll and his son, George W. Carroll, contributions of $75,000 each to construct a chapel and library building and a science hall. These were the largest single donations to education in Texas history up to that time. In addition to enhancing the reputation of the University and acquiring funds to construct must needed facilities, Cooper was moderately successful in reducing Baylor's indebtedness.
On March 31, 1902 Cooper suddenly resigned, probably because of an incident with a small dog in chapel. According to J. M. Dawson, a student at the time, "some prankish students sneaked a howling dog into the small upstairs chapel on the lofty third floor of Main. When the perverse little animal disturbed the worship the president became enraged. He (Cooper) leaped down from the platform, seized the dog and hurled it through a window to the ground below. The act appalled everybody, because it showed a lack of control deemed inexcusable, although under most exasperating circumstances."
Cooper apologized for his rash action, but according to Dawson "a gifted pugnacious youngster named J. Frank Norris led a sensational student uprising against him." The final result was the tendering of his resignation at a called meeting of the trustees.