Even though the Civil War interrupted his education, he still served as a wartime surgeon. Military records indicate that his initial service was with the 1st Florida Battalion from February of 1862 until June of 1862. His next assignment in September of 1862 was to the 7th SC Infantry of Kershaw's ANV brigade. He resigned from this position in April of 1863 but on July 20th 1863 was assigned as the surgeon of the Phillips Legion Infantry Battalion. He continued in this assignment until November of 1864 when he was granted a 30 day leave. Entries in July of 1864 show him as the senior surgeon of Wofford's brigade (of which the Legion was a part). Although this is the final entry in his record, it would appear he remained in this assignment until war's end.
After the war he completed his education, earning a Doctorate of Medicine from the University of Georgia. Dr Shine commenced his residence and medical practice in 1867 at St Augustine, Florida. In 1868, William married Maria Jefferson Eppes. Their only child, Francis Eppes Shine was born in 1871 and would also become a doctor. William's wife died in 1897. He lived on until October 21, 1910. Dr Shine and his wife are buried together at Greenwood Cemetery in Orange County, Florida.