In 1890, Louisiana passed a statute called the Separate Car Act, which stated "that all railway companies carrying passengers in their coaches in this state, shall provide equal but separate accommodations for the white, and colored races, by providing two or more passenger coaches for each passenger train, or by dividing the passenger coaches by a partition so as to secure separate accommodations. . . . " The penalty for sitting in the wrong compartment was a fine of $25 or 20 days in jail.

The Plessy case was carefully orchestrated by both the Citizens' Committee to Test the Constitutionality of the Separate Car Act, a group of blacks who raised $3000 to challenge the Act, and the East Louisiana Railroad Company, which sought to terminate the Act largely for monetary reasons. They chose a 30-year-old shoemaker named Homer Plessy, a citizen of the United States who was one-eighth black and a resident of the state of Louisiana. On June 7, 1892, Plessy purchased a first-class passage from New Orleans to Covington, Louisiana and sat in the railroad car designated for whites only. The railroad officials, following through on the arrangement, arrested Plessy and charged him with violating the Separate Car Act. Well known advocate for black rights Albion Tourgee, a white lawyer, agreed to argue the case without compensation.

In the criminal district court for the parish of Orleans, Plessy argued that the Separate Car Act violated the 13th and 14th Amendments to the Constitution.

13th Amendment
Section 1. Neither slavery nor involuntary servitude, except as a punishment for crime whereof the party shall have been duly convicted, shall exist within the United States, or any place subject to their jurisdiction.

14th Amendment
Section 1. All persons born or naturalized in the United States and subject to the jurisdiction thereof are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws. 

John Howard Ferguson was the judge presiding over Plessy's criminal case in the district court. He had previously declared the Separate Car Act "unconstitutional on trains that traveled through several states." However, in Plessy's case he decided that the state could choose to regulate railroad companies that operated solely within the state of Louisiana. Therefore, Ferguson found Plessy guilty and declared the Separate Car Act constitutional.

Plessy appealed the case to the Louisiana State Supreme Court, which affirmed the decision that the Louisiana law as constitutional. Plessy petitioned for a writ of error from the Supreme Court of the United States. Judge John Howard Ferguson was named in the case brought before the United States Supreme Court (Plessy v. Ferguson) because he had been named in the petition to the Louisiana Supreme Court and not because he was a party to the initial lawsuit.