Death tolls began increasing, both from the disease and some then-common treatments for it (such as mercury injections), as the city's population grew following its return to French rule in 1800 and cession to the United States as part of the Louisiana Purchase three years later.

The Union Navy's blockade of New Orleans six years later, as the Civil War began, the city for the first time in the century recorded no deaths from yellow fever.

In 1882 the Louisiana legislature amended the statutes to require that vessels stopping at the quarantine station pay as much as $30 ($900 in today's dollars[3]) in fees, depending on their size, with the proceeds going to fund the board's operations and infrastructure.

One New Orleans–based shipper challenged this in court as a tonnage tax, which they called an unconstitutional violation of the Commerce Clause since the federal government alone had authority to levy one; they further alleged that it was being used for the city of New Orleans' general revenue rather than its stated purpose.

[4] "If there is a city in the United States which has need of quarantine laws, it is New Orleans", Justice Samuel Freeman Miller, a physician prior to his legal career,[5] wrote for the Court.

Many of the ships that came to New Orleans from the Gulf often came from warmer countries to the south, where tropical diseases were common, and past epidemics of yellow fever and cholera in the Mississippi Valley had all been identified as having spread from the city.

[7] Among the many reasons the Italian immigrants were considered undesirable was the belief that they brought diseases into the U.S.[8] In September 1897 a yellow fever outbreak believed to have originated in Ocean Springs, Mississippi, spread to New Orleans, where it led to a single death and several cases.

[2] A year after the 1897 outbreak, the SS Britannia, owned by the French corporation Compagnie Française de Navigation á Vapeur, left the Sicilian port of Palermo carrying cargo and Italian emigrants, along with some returning U.S. citizens.

In late September, the vessel duly stopped at the quarantine station, near Fort Jackson, where all 408 passengers and the ship's cargo were certified as free from disease and allowed to continue to New Orleans.

[12] After the court dismissed the petition for failure to show cause, the Britannia took its passengers to Pensacola, Florida, to put off and returned to New Orleans, where it unloaded its cargo.

Lastly, the company argued, the order barring the landing of the passengers was a denial of its equal protection and due process rights under the Fourteenth Amendment.

[16] Again, the district court dismissed the case after the board of health made a peremptory plea arguing no cause of action existed for Compagnie Francaise.

During the 1897 outbreak, Italian emigrants had continued to arrive in New Orleans by boat, but despite "excited public discussions", the board had concluded it lacked the power to prevent their entry at the time.

"[22] Nicholls found Compagnie Française's due process arguments "utterly untenable" as the board's action was necessary under the law; he wondered rhetorically what else it could have done.

The passengers had been inconvenienced, he agreed, and the company forced to incur extra expenses, but that was damnum absque injuria, meaning it could not recover from the state.

[24][25] Compagnie Française had offered "a most copious reference" to cases where the Court had held states to have overreached into Congress's domain in their regulations of commerce, White observed.

"[T]he contention demonstrates its own unsoundness", he wrote, since it amounted to a theory that either the Fourteenth Amendment had eliminated the police power, or had rendered it unusable.

But, White noted, the same section of the treaty allowed for local authorities to quarantine the ship on arrival, either as part of a general measure or if it specifically was found to have sick passengers.

"[31] The Court should have looked not to Morgan's as a precedent, Brown argued, but instead to an earlier case, Railroad Company v. Husen, which the majority was "directly in the teeth of".

The same section of the treaty with Greece that the majority had relied on in dismissing the petitioners' argument also had a provision he quoted, stating that ships with the required documentation from health officers at the port of embarkation were free from disease "shall be subjected to no other quarantine than such as may be necessary for the visit of the health officer of the port where such vessels shall have arrived, after which said vessels shall be allowed immediately to enter and unload their cargoes."

[10] In 2016 New Jersey federal district judge Kevin McNulty cited Compagnie Francaise, among other cases, in holding that existing case law on quarantines was sufficient to sustain state officials' defense of qualified immunity in a suit against them brought by Kaci Hickox, a nurse quarantined for 80 hours after she showed a fever upon her return to Newark International Airport from Sierra Leone, where she had been treating victims of the 2014 Ebola outbreak.

It noted that, as it was at that time, the federal government still largely delegates that power to state and local authorities, which it was concerned could complicate a centralized response to any outbreak.

[38] During the pandemic, Michigan Court of Claims Chief Judge Christopher Murray dismissed a challenge to Governor Gretchen Whitmer's stay-at-home order.

He noted that contrary to the petitioners' claim that the Supreme Court had never held restrictions on the movements of healthy individuals during a pandemic constitutional, it had done just that in Compagnie Francaise.