On September 16, 1893, during the Panic of 1893, fifteen men formed the Savings and Loan Association of Topeka, including "bankers, insurance agents, attorneys, railroad employees, the president of a dry goods store, the Topeka City School Superintendent and a physician."

In 1938, the organization underwent another name change, becoming the Capitol Federal Savings and Loan Association.

On December 9, 1961, Capitol Federal opened a new headquarters location in Topeka, complete with a fallout shelter as a civil defense measure during the Cold War.

In 1975, Capitol Federal became the second savings and loan institution to offer its customers account access outside of its buildings.

[5] In January 2009, John C. Dicus reached 50 years of employment with Capitol Federal, the board's mandatory retirement age.

This decision faced some criticism, with many people opposing the growing trend of corporate names on school buildings.

[7] In 2015, Capitol Federal upgraded its debit cards to include EMV chips and Apple Pay support.