Most of the changes are billed as improvements, although SBB warned customers will have to change their habits in some cases and “get used to new routes in the Greater Zurich area”.
The timetable change on December 13th is the most ambitious since the Rail 2000 programme was launched in 2004, the rail operator said.
The recently opened underground station in Zurich will enable quicker links in the region, as well as cross-country trains.
More routes are being added to Zurich's S-bahn local train network, though bids to improve punctuality mean that some train times will be longer.
Trips from Geneva in the west of the country to Saint Gallen in the northeast will be cut by 18 minutes, bringing the fastest connections to three hours and 46 minutes.
In many regions more rush-hour trains will be available but work to upgrade Lausanne's station will have a negative impact on service in French-speaking Switzerland.
Trains between Geneva and Lausanne will take three minutes longer, while reductions in service are planned between Lausanne and the canton of Valais.
SBB noted that Léman 2030, a three-billion-franc expansion project between Lausanne and Geneva, will be carried out over the next ten years.
This will mean changes in the Jura where direct trains to Geneva will be eliminated in favour of liaisons via Biel/Bienne, while half-hourly service will replace trains once an hour from Neuchâtel to La Chaux-de-Fonds.
Among the new services planned is an extension of the Simplon car-carrying service, which runs now from Brig to Iselle, to include trips to the Valais and Italy every 90 minutes.
The Swiss Federal Office of Transport has opened a consultation phase on the 2016 schedules for trains, cableways, boats and buses in a bid to iron out any “discrepancies” in the times.
The timetable can be viewed (in French, German and Italian) at www.fahrplanentwurf.ch.
Customers have until June 14th to point out discrepancies through written or online comments.