Flanigan was established in 1909 with the building of the Western Pacific Railroad Feather River Route between Oakland and Salt Lake City.

[3] The station in Honey Lake Valley was named after Patrick L. Flanigan, a landowner and businessman whom Western Pacific purchased right of way from in the area.

[12] By fall 1960, only one permanent resident remained, schoolteacher Gertrude Milne, who tended the store and taught 7 children from surrounding areas.

[17] Later in the 1970s, investors bought land just east of Flanigan, established dirt streets and planned to sell parcels for $200-$300 each, as a novelty to capitalize on Flanigan's Western ghost town history, intending to give parcels to celebrities like John Wayne and Clint Eastwood to draw publicity.

However, the Interstate Land Sales Full Disclosure Act of 1968 requires new developments with plots sold over $100 to have basic infrastructure such as sewer and street lighting, which made the plan unprofitable, and the venture was abandoned.