Cook was born in Twiggs County, Georgia. His parents had moved from Virginia to Georgia. He served with the United States Army in the Seminole Wars, serving in Florida. After studying at Oglethorpe University, he graduated from the law school of the University of Virginia in 1841. He subsequently lived in Macon County, Georgia, where he maintained a law practice.
Once the American Civil War started, Cook sided with the Confederate States of America and enlisted as a private in the 4th Georgia Volunteer Infantry. By the end of the Seven Days Campaign on the Virginia Peninsula, Cook had advanced to the rank of lieutenant colonel. He also fought in the battles of Second Manassas, Antietam, the Second Fredericksburg and Chancellorsville, where he was wounded in the leg. As a result, he missed the Gettysburg Campaign while he recovered.
For a short time, Cook took a leave of absence to serve in the Georgia Legislature before returning to the army. At the Battle of Cold Harbor in 1864 he took over the brigade when Brig. Gen. George P. Doles was killed. Cook was wounded again during the Siege of Petersburg. After recovering, he fought under Maj. Gen. Stephen D. Ramseur at the Battle of Cedar Creek in the Shenandoah Valley before returning with his men to the trenches around Petersburg, Virginia. He was wounded a third time during the 1865 attack on Fort Stedman.
After the war ended in early 1865, Cook moved to Americus, Georgia, where he set up a law practice and was active in local and state politics. From 1873 to 1883, Cook was a member of the United States House of Representatives, serving a district comprised of part of southwest Georgia. He became Georgia's Secretary of State in 1890 and was part of the commission that built Georgia's state capitol building in Atlanta.
Phillip Cook died in Atlanta on May 21, 1894. Cook County, Georgia, is named in his honor.