[4] Upon the passage of the Kansas–Nebraska Act on May 30, 1854, President Franklin Pierce appointed Lecompte to the position of Chief Justice of the Supreme Court of the newly organized Kansas Territory.

[5]: 423  Upon arriving in Kansas, he, alongside Daniel Woodson, sponsored the foundation of the proslavery stronghold of Lecompton, which was named after him by his supporters.

Lecompton was named the capital of Kansas Territory by the Bogus Legislature on August 8, 1855, after Pawnee's bid was sabotaged by Woodson and his proslavery allies, who objected to Pawnee's distance from the critical Missouri bases of the Border Ruffians, and sought to gain financially from naming a city whose land they controlled.

[6]: 75–80 Upon the bloodless resolution of the Wakarusa War in December 1855 between pro- and anti-slavery settlers, Congress appointed three representatives to the newly created "Committee to Investigate the Troubles in Kansas".

[7]: 433 Matters in Kansas were further complicated by the formation of a rival government under the free-state (anti-slavery) Topeka Constitution in January 1856, and so there existed, concurrently, two rival Governors of Kansas: the proslavery Wilson Shannon, based in Lecompton and recognized by the Federal Government, and the free-stater Charles L. Robinson, based in Lawrence and seen by President Pierce as the leader of a "treasonable insurrection".

[7]: 417 Accordingly, Lecompte surprised the Committee by convening, on May 5, 1856, a grand jury which resulted in the indictment of all members of the "Topeka Government" on charges of treason,[8] and arresting Governor Robinson while he was traveling by steamboat in Lexington, Missouri.

Deputy Marshal W. P. Fain entered Lawrence with 8 men and served the indictment papers without incident, and disbanded the posse.

[7]: 435  The Hotel was bombarded by three cannons and a powder keg was detonated inside, and when that failed to damage the structure, it was burned down, but not before the rooms and the liquor stock were ransacked by the attackers.

[7]: 313, 389  Sol Miller, the editor of the Troy Kansas Chief newspaper, said in 1874 that Lecompte was the judge "the very mention of whose name, less than twenty years ago, caused a shudder everywhere in the Free States".