Commerzbank, Germany's second-biggest lender, announced Thursday that it will start charging large corporate customers and institutional investors to hold a high level of deposits on their accounts.
However, individual private customers and small and medium-sized businesses would not be affected, the bank insisted.
"We reserve the right to charge some large corporates a fee on parked liquidity" above a certain threshold, Commerzbank said in a statement.
The move comes following a decision by the European Central Bank in June to take its key interest rates into negative territory for the first time.
The ECB slapped a negative rate on bank deposits placed overnight at the central bank, meaning financial institutions must pay to keep their surplus reserves there.
The ECB hoped the move would persuade banks to lend the money on to the private sector rather than parking it at the central bank.
In September, the ECB moved the rate deeper into negative territory, cutting it to minus 0.2 percent.
One of the risks of negative interest rates is that banks may attempt to recoup the extra costs from their customers.
Commerzbank said it would encourage large clients to shift extra cash to alternative investments.
Negative interest rates are highly controversial in Germany, where households and many companies prefer dull but stable saving accounts to investing in the stock or bond markets.
Skatbank, one of the country's many small banks, recently announced plans to charge retail and business customers with more than 500,000 euros in deposits a negative interest rate of 0.25 percent from November 1.
But Commerzbank is the first major bank to do so.
Germany's biggest lender, Deutsche Bank, said it has "no current plans to introduce fees for deposits in retail banking."
"For institutional clients with an additional need for deposit-related products, the bank offers various investment alternatives to appropriately react to the changed interest rate environment. Investment alternatives on offer include term deposits," a spokesman said.