The daily count rose to 1,002,000, 3.7 percent more than in 2012.
The higher numbers were down to expanded services during what SBB described as a “difficult year”, resulting in overall net income tumbling to 238.2 million francs from 422.4 million francs in 2012.
The lower earnings came despite a 14.7-million-franc surplus from SBB Cargo, the first positive result in 40 years for the division.
Accidents and the impact of construction and maintenance work “adversely affected punctuality and customer satisfaction”, SBB acknowledged in a news release.
Punctuality was “high” at 87.5 percent in 2013 but this was below the 88 percent rate registered the previous year, the rail operator said.
The number of passenger-kilometres travelled rose 1.3 percent to 17.8 billion.
The increase was largely due to improved services in French-speaking Switzerland, with 30 percent more seats and 14 additional trains, SBB said.
More frequent service between Zurich and Schafhausen, now twice an hour, is also credited with boosting passenger totals.
Fare increases that came into effect in December 2012, up by an average of 5.2 percent, boosted revenues by 129 million francs, the rail operator said.
But operating expenses rose by more than 332 million francs, driven by higher “train-path” costs and maintenance.
SBB, which employs 31,000 people, said it was continuing its programme of modernizing train stations, with developments under way in Lausanne and Geneva.
Real estate development of rail properties is also continuing, it said.
By 2020, Zurich’s new Europaallee district, being developed by SBB, will include 400 apartments, a hotel and more than 50 news shops and restaurants, creating 6,000 jobs.
The first phase of Zurich’s cross-city link and the new underground station at Löwenstrasse are set to come into service in mid-June, which will provide faster and more frequent S-Bahn services, SBB said.
It said ground will broken on the Léman 2030 project, which promises to significantly improve rail services in French-speaking Switzerland, eventually doubling seat capacity between Lausanne and Geneva.