With Burleson's departure to head what soon became known as Waco University, the leadership reigns of Baylor University passed to George Washington Baines, a prominent figure in Texas Baptist circles. Born in North Carolina in 1809, Baines had arrived in Texas in 1850 via Georgia, Alabama, Arkansas and Louisiana, preaching and teaching along the way as well as serving a brief stint as an Arkansas legislator.
A former member of the Baylor Board of Trustees (1851-59), he and his wife had served a short time as house parents of the boarding house for the female division of the University. He had left his Baylor employment when Graves resigned to follow him as pastor of the Independence Baptist Church and then a short time later he accepted the editorship of the newly established denominational newspaper, the Texas Baptist.
Baines agreed to lead Baylor for a year while the trustees searched for a more suitable replacement for Burleson. He did his best to recruit teachers and students, but with the coming of the Civil War, he had little success. Records are unreliable as to the number of students enrolled during his administration, but it is known that at least 151 male students and several faculty members left the University during his first year to join the Confederate cause. One coed wrote at that time, "You can drive all across town and not see a single young man."
After Baines' first year, the trustees found it difficult to find anyone to lead the financially-plagued university and pleaded with Baines to continue as president. He wanted relief from his duties because of his health and because of the amount of time he had to devote to teaching and personally directing various University operations, but he agreed to stay if "we could employ a competent teacher to take charge of the primary classes, then I could hear recitations four hours, as it is usual in colleges, and have time for literary preparations and relation."
The trustees immediately found another teacher who was hired "with the provision that he is to look to the endowments and tuition for his salary" (in other words, he could teach at Baylor, but he would also have to raise the money for his own financial compensation). As a result, Baines reluctantly remained at the helm of the school for another year. It would be a year of hardship with most of his efforts spent to maintain the status quo, which unfortunately kept slipping downward with each day that the war lingered.