In a memorable referendum on 20 February 1898, voters approved the "Federal Act on the Acquisition and Operation of Railways on Behalf of the Confederation and on the Administrative Structure of Swiss Federal Railways" by 386,634 votes in favour to 182,718 votes against. The debate in the run-up to the vote was extremely lively. Under the slogan "Swiss Railways for the Swiss People", the supporters stressed the advantages of standardisation if the railways were under national control. The opponents of the draft legislation warned against an additional army of officials, which, they claimed, would increase the power of the state and ruin its finances at the same time.

The Board of Directors of SBB was constituted in October 1900. It consisted of no less than 25 members appointed by the Federal Council, with another 25 appointed by the cantons and half-cantons and four members elected by the district railway boards. In November 1900, a contract on the direct purchase of Schweizerische Centralbahn (SCB) was drawn up by the federal government. The Federal Assembly consented to the acquisition on 14 December 1900. It was now a matter of urgency, because the transaction was to become legally effective at New Year 1901. Consequently, the first train arriving in Berne from Zurich, Aarau and Olten at 2am on New Year's Day 1901 received a ceremonial welcome prior to continuing its journey to Lausanne and Geneva. To begin with the SCB routes were still operated by SCB staff on behalf of the federal government. In mid-1901, the management board of SBB replaced the Federal Railways Department as the regulatory authority of the SCB.

As the Swiss North-East Railway (NOB) also came under SBB's wing on 1 January 1902, this date is regarded as Swiss Federal Railways' "official" birthday.