The presidential order on Tuesday was part of Washington's latest efforts to pressure Pyongyang into resuming multi-party talks on disarming its nuclear arsenal.
The US aims to use tougher new sanctions to prevent suspect North Korean entities from obtaining financial and commercial means to "develop nuclear weapons and the missiles capable of delivering them".
"Any assets of the entities designated today that are within US jurisdiction must be frozen," the statement said.
"Additionally, US persons are prohibited from conducting any transactions with these entities."
The two entities were earlier blacklisted by the UN in July for their role in North Korea's weapons of mass production and missile programs, it said.
The GBAE oversees North Korea's nuclear programme and manages operations at the Yongbyon nuclear plant, while the trading firm helps procure commodities and technologies for defence research, development and procurement.
The move came as North Korea marked the 61st anniversary of its founding on Wednesday with patriotic songs and praises to Kim Jong-il, the leader of the communist state.
Thousands of North Koreans marched to historical landmarks in the capital as television broadcasts aired songs calling for eternal loyalty to Kim, who missed last year's celebrations due to a suspected stroke.
In recent days the US has made overtures in an attempt to get North Korea back to the six-party talks but the North continues to wrongfoot the international community with conflicting messages about its nuclear programme.
Last week the North said it had reached the final stages of enriching uranium and was also building more plutonium-based atomic weapons.
North Korea in April quit six-party talks with South Korea, the US, Japan, Russia and China in protest at the international censure of a rocket launch.