On December 14, 1945, Lynne was nominated by President Harry S. Truman to a seat on the United States District Court for the Northern District of Alabama vacated by Judge Thomas Alexander Murphree. Lynne was confirmed by the United States Senate on December 20, 1945, and received his commission on January 3, 1946. In 1953, he became the Chief Judge of the court. Lynne was involved in a number of civil rights cases during his service. On June 5, 1956, in the Browder v. Gayle case, the District Court ruled 2-1, that bus segregation is unconstitutional under the Equal Protection Clause of the 14th Amendment to the U.S. Constitution. Lynne write the dissenting opinion in the case. In this case, Lynne's dissent was based on his belief that Brown v. Board of Education desegregated only educational facilities; but for other public services Plessy v. Ferguson remained in effect. This was the first case that extended desegregation to additional facilities, effectively overruling the Supreme Court in Plessy. In 1957, in the Baldwin v Morgan case, Judge Lynne refused to order the desegregation of waiting rooms at Birmingham Terminal Station after two black residents were arrested for using the whites-only facilities. The plaintiffs' attorney, Oscar Adams, sought a summary judgment to desegregate the waiting rooms. His view was that no law compelled the passengers to observe the signs and, so while their arrest was improper, there was no further action to be taken as this was not legally segregated. His ruling was overturned by the United States Court of Appeals for the Fifth Circuit on appeal in 1961. Lynne heard two cases on school desegregation in Birmingham, Shuttlesworth v. Birmingham Board of Education in 1958 and Armstrong v. Birmingham Board of Education in 1963. In both cases, Birmingham schools officially did not discriminate on school admissions based on race, but implemented an achievement test that resulted in black students being denied admission to all-white schools. Lynne denied the plaintiff's request to overturn the school admission standards because the plaintiffs had not exhausted all of their remedies. After the case was appealed, the Fifth Circuit overruled Lynne and ordered him to issue a ruling to desegregate the schools. As an added complication, Lynne, as the Chief Judge, imposed a procedural rule that out-of-state attorneys had to associate with a local law firm in order to argue a case in the court. In one case, a local attorney was pressured to sever his ties with the black lawyers, depriving them of an opportunity to have cases heard in Lynne's Court. In 1963, he ordered Governor George Wallace, who had promised to block the entrance doors of the University of Alabama to prevent black students from registering, to allow Vivian Malone Jones and James Hood to enter the university, ending segregation at that institution. Lynne's ruling emphasized that law and order had to be maintained and that Wallace could not prevent enforcement of the laws. His views on civil rights did change somewhat over time. In Washington v. Lee of 1966, his court overturned racial segregation in prisons, requiring integration of all facilities. His ruling was upheld by the Supreme Court in 1968. In 1973, Judge Lynne took on senior status and continued to hear cases until 2000. In 1995, the federal courthouse in Decatur, Alabama was renamed in his honor. Lynne died on September 10, 2000 in Birmingham.
