The Bank is imposing a rate of minus 0.25% on "sight deposits" - a form of instant access account - of more than 10m Swiss francs ($9.77m).
It is trying to lower the value of the Swiss franc, which has risen recently.
Russia's market meltdown and a dramatic plunge in the oil price have led investors to seek "safe havens".
The announcement sent the franc lower, and in early trading the euro was buying 1.201 Swiss francs, fewer than the 1.203 it was worth before the news, just within the target.
Switzerland typically sees money flow in during economic uncertainty.
The new rate will be introduced on 22 January and will only affect banks and large companies who use the "sight account" to transfer funds quickly and without restrictions.
A negative rate means depositors pay to lend the bank their money.
Geoffrey Yu, a currency strategist at UBS, said: "In the short term it gives them some breathing space.
"If you hold Swiss francs right now you do have to bear a cost. New buyers will be forced to think twice."
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