[4] He graduated in due course and on July 10, 1846, was ordained deacon by William Meade and assigned to the historic Lynnhaven parish[5] near Virginia Beach, which also operated a free school pursuant to the bequest of its rector who had died as the American Revolution began.

[7][8] In 1859, while attending the General Convention in Richmond during the controversy over John Brown's raid on Harpers Ferry, Lay was elected missionary bishop of the Southwest, with jurisdiction over "Arkansas, the Indian territory, Arizona and New Mexico", and consecrated by Meade, Cobbs, Leonidas Polk, Stephen Elliott and several others on October 23, 1859.

After an exploratory trip around his new diocese (which extended west to Phoenix, Arizona), Lay decided to make his base in Fort Smith, where Polk had established Christ Church in 1840.

[9] After returning to Huntsville for the birth of his son, Lay went on an extended tour from Savannah, Georgia to New York City to raise funds for his missionary work.

In the summer of 1860, Lay moved his wife, four children and three slaves (including a newly purchased twelve-year-old named Lizzy) to Fort Smith, where a gift from a Virginia cousin enabled them to buy a small house so they could plant a vegetable garden and keep pigs, a chicken and a cow.

Lay returned home from a diocesan tour to check on his family, then decided to advise his clergy that they no longer needed pray for the President.

For the next four years, the Lay family never again settled — traveling first to Little Rock, then returning to Huntsville shortly before its capture by federal forces under General Ormsby Mitchell in April 1862.

He left his eldest son (Henry Jr.) in a Virginia boarding school in October, and proceeded to Augusta, Georgia to attend the first General Council of the Protestant Episcopal Church in the Confederate States of America.

[16] After the city fell, General William Sherman gave Lay permission to cross Union lines to visit his wife and return.

He even managed to visit Union Generals Ulysses Grant and George Meade at City Point under a flag of truce during the Confederacy's final months.

Lay was then released, provided with train fare home, and managed to reach Lincolnton in time to for the birth of another daughter on September 25, 1865.

Thus, after the General Convention still acknowledged Lay as Bishop of the Missionary District of the Southwest, he returned to his diocese, landing at Helena, Arkansas circa 3 a.m. on December 31, 1865.

Disappointed to find "not one open church, not one clergyman officiating," Lay rallied the impoverished and discouraged congregations and convinced clergy to return.

His flock gave their departing bishop the altar cross from the century-old parish in Pine Bluff, Arkansas, inscribed with the last verse of Psalm 78: "So he fed them according to the integrity of his heart; and guided them by the skillfulness of his hands.

[36] His traveling communion set from his days as missionary bishop, and other artifacts, were left with the Diocese of Easton, where they are often displayed at Bray House.

His grandson Beirne Lay, Jr. became an early Army aviator, and writer in response to the Air Mail Scandal, then distinguished himself in World War II and later as a screenwriter.