Tom married Mary Elizabeth Douglas (daughter of Rev. Alexander Douglas of Smith County, Texas) on June 6, 1856 in Smith County, Tx. The Broughton couple had seven children. Tom supported his family with his law practice which continued to grow steadily in Athens, but in 1859, he and his brother D. W. moved their practice to Kaufman, Texas where they partnered with another attorney, R. H. English.

In 1861 he joined the Confederate Army, enlisting in a group called the Texas Wide Awakes which was organized in Kaufman County, in Captain Jack Wharton's company. The company mustered in Marshall and in October moved to Hopkinsville, Kentucky, where it became part of the 7th Texas Infantry commanded by Col. John Gregg. Broughton became Captain of Company C. The 7th Texas was sent to Fort Donaldson, Tennessee where a four-day fight ended with the Confederate fort surrendering to General U. S. Grant. As a prisoner of war, Tom spent time at Camp, Camp Chase and Johnson's Island near Sandusky, Ohio.

In September of 1862, he was taken to Vicksburg where on the 26th, he was exchanged. After his release, Tom came home briefly to recruit and then in December 1862 he went to Port Hudson, Louisiana where he joined confederate forces to battle Farragut's bombardment of the fort with gunboats. The Battle of Raymond, May 12, 1863, had been an engagement Gregg's Brigade thought they would easily win. However, Confederate scouts had miscalculated the size of the approaching Union forces and instead of a single brigade, found themselves facing the entire Seventeenth Corps, numbering some 12,000 soldiers. Against such odds, there was no way the Confederates could win. After five or more hours of intense fighting, General John Gregg called for a retreat. As Gregg and his men retired from the battlefield, they looked back on what could only be described as a horrific scene. Approximately 335 Confederates, including 25 officers and 300 enlisted men, lay dead or wounded. Incapacitated, the wounded had to watch as their brigade filed from the battlefield, leaving them in the hands of the enemy. By nighttime, as the roll was called, an additional 190 men were reported captured or missing in action. Captain Broughton, 7th Texas Infantry, was last seen leading his men in an attack near Fourteen Mile Creek. Three days later Colonel Granbury, commander of the 7th Texas, reported, "I omitted to state that Captain E. T. Broughton, Company C, was among the last to leave the creek, having animated his men throughout the affair with his presence and bearing. He is among the missing." He had been captured near Fourteen Mile Creek and taken to the Oak Tree Hotel, a makeshift prison in Raymond. Here, he was thrown in the room with another prisoner, Sgt. Patrick Griffin, 10th Tennessee Irish. Broughton and Griffin were no strangers. Both had been captured at Fort Donelson. In a few days, along with other prisoners taken during the Battle of Raymond, Broughton and Griffin were loaded on a passenger boat heading north. Once again, a northern prison awaited them. Griffin managed to escape while docked at Two-Mile Island near Memphis. Eventually, he worked his way back to his regiment. Broughton was not so lucky. He was transported back to Johnson's Island where he was incarcerated for another year. During this time, he fell ill with smallpox, an illness that left him almost blind. It was in this physical condition that he was again exchanged in May of 1864.

On May 8, 1864, Broughton was exchanged and returned to his regiment, which had spent the winter quartered at Tunnel Hill, Georgia. In spite of his weakened condition, Broughton continued to fight through the Battle of Atlanta then moved on with General John Bell Hood's army toward Nashville. On November 30, 1864, after General Hiram B. Granbury was shot from his horse during the Battle of Franklin, Broughton took command of "Granbury's Texas Brigade." Following the Tennesse Campaign, the nearly blind and wounded Broughton suffering from "obstinate chronic conjunctivitis and general debility" resigned his command on January 16, 1865. He was granted leave of absence pending action on his resignation.

Broughton returned home and resumed his law practice. In 1869, he was elected to the Texas state senate, representing the 22nd District. He held the post for two terms and would have successfully run for another term but failing health forced him to the sidelines. Physically, Broughton never recovered from the illnesses he contracted on Johnson's Island. E. T. Broughton passed away in Sherman, Texas, shortly before his 40th birthday. His obituary in The Sherman Courier February 12, 1874, read, "He won his military title by service in the Confederate Army, answering to the first call made by the troops, and remained by his flag he loved until all was lost, save honor."