The measure will take effect on September 2.
Vytautas Valvonis, director of the central bank's Supervision Service, says people often choose these complex financial derivatives without understanding what they are investing in.
"We will now use tools that enable us to ensure that they are simply not available to them or that risk is minimized," he said in a press release.
The EU's new Markets in Financial Instruments Directive allows national supervisors to ban or restrict products and services affecting non-professional investors.
Studies by EU bodies show that 74-89 percent of non-professional investors trading in CFDs suffer losses ranging from 1,600 euros and 29,000 euros per client on average.
According to the Bank of Lithuania, other EU member countries intend to introduce similar measures.