WASHINGTON — President Obama has chosen the Treasury Department official who has directed the effort to cut off funding of the Islamic State and impose economic sanctions on Syria, Russia and Iran to become the C.I.A.’s deputy director, the agency announced on Friday.

The official, David S. Cohen, who as under secretary for terrorism and financial intelligence has spent more than three years in charge of the Obama administration’s attempts to punish foreign governments and cripple terrorist groups, will help lead an agency that remains at the center of armed drone campaigns and covert efforts to arm and train Syrian rebels.

John O. Brennan, the C.I.A. director, said in a statement that Mr. Cohen brings a “wealth of experience on many of the issues that we focus on as an agency” — such as money laundering, financial support for terrorism and narcotics trafficking.

In the past, the C.I.A.’s No. 2 job, which does not require Senate confirmation, has often been filled by agency veterans or senior military officers. Mr. Cohen, a lawyer who has no previous C.I.A. experience, will replace Avril D. Haines, who left the C.I.A. to become Mr. Obama’s deputy national security adviser.