Lynch was born in Baltimore, Maryland. His mother was a slave, and his father was a white merchant and minister. Lynch obtained his early education at an elementary school instructed by Rev. Daniel Payne of the African Methodist Episcopal (AME) Church. Lynch attended Kimball Union Academy in New Hampshire, where he spent two years, and then moved to Indianapolis where he committed himself to ministry. Of the northern schools prior to 1860, Kimball Union Academy, was one of the few schools in which allowed African Americans students to attend. He preached in the town of Galena, Illinois at a small church.
In 1863, he was appointed a "Missionary and Government Superintendent" at Beaufort, South Carolina. Following the Civil War, Lynch later joined other missionaries in South Carolina. Between 1865 and 1866, Lynch helped to establish churches and schools in South Carolina and Georgia for African American children and adults. In 1868 Lynch then moved to Mississippi as an official of the Methodist Episcopal Church North. Within a year of Lynch’s arrival, the church increased by approximately six thousand African Americans, and twenty meeting houses were created. Soon Lynch began to realize that the political rights of the freedmen were just as important as their religious faith. Lynch and others organized the Republican Party in Mississippi, where they later held the first party convention in September 1867 in Jackson. At this time Lynch was elected Vice-President of the organization because of his prior services to the party. Lynch then worked to creating a new constitution for Mississippi, where he took a moderate stance. He campaigned to secure voter support for a constitutional convention, in addition to verifying the election of Republican delegates. To further stress his position and the importance of black unity, Lynch became involved with the newspaper business, and became a publisher and editor of his publication called Jackson Colored Citizen.
During the organization of the [1868 "Black and Tan"] convention, it was moved that the word "colored" be added to the name of each Negro delegate. Thereupon, the Reverend James Lynch, a colored man, afterward Secretary of State, moved to amend it so that the color of each delegate's hair should be added also.
In 1869, Lynch was elected Secretary of State, after defeating his convention rival, Dr. Thomas W. Stringer, by a vote of 158 to 36. As a result, in the State of Mississippi, Lynch became the first African American official. While Secretary of State, Lynch had to pay for some of the expenses out of his own pocket because people previously believed that it did not take much to run an administrative department. In office, Lynch improved the public school system throughout the state and acquired support from whites. In 1871, Lynch was re-elected as Secretary of State. In 1872, he served as a delegate to the National Republican Convention. While in his second term, Lynch and his African American supporters, started to become disillusioned with the Reconstruction process, along with the increasing tension amongst the African American and white Republicans.
Also in 1872, Lynch was troubled with Bright’s disease of the kidney, accompanied by the recurrence of pneumonia. On December 18, 1872, James Lynch died at the age of thirty-four. Lynch received a state funeral, in which the governor of Mississippi, R.C. Powers, was one of the pallbearers. Lynch was buried at Greenwood Cemetery in Jackson, Mississippi, where city and state officials, three black fire brigades, a black charitable order, Friendly Brothers, and a large concourse of African Americans followed the procession to the grave. The Republicans, who still controlled the state legislature, later passed a bill appropriating a thousand dollars for the erection of a monument.1881, The Bench and Bar of Mississippi