Brunson risks up to 35 years in jail if convicted of carrying out activities on behalf of two organisations Turkey deems to be terror groups: the Gulen movement and the Kurdistan Workers' Party (PKK).
In a briefing for reporters after the sanctions were announced, White House spokeswoman Sarah Huckabee Sanders said that Trump was "not happy with Turkey's decision not to release Pastor Brunson" and had directed the Treasury Department to impose the measures.
He also said his foreign minister, Mevlut Cavusoglu, would hold talks with U.S. Secretary of State Michael Pompeo on the sidelines of an ASEAN meeting in Singapore.
Last month Trump hit out on Twitter at Turkey over its decision to keep the pastor in custody after a Turkish court denied a request for the release of Andrew Brunson.
Turkey blames the 2016 coup attempt on Fetullah Gulen, a Turkish cleric now living in the United States, and has long suspected that Washington had a hand in it-allegations the United States fiercely denies.
The two officials targeted by sanctions "played leading roles in the organizations responsible for the arrest and detention" of Brunson, the US Treasury's Office of Foreign Assets Control (OFAC) said in a statement. The sanctions against them prohibit US citizens from doing business with both men and block any of their property that rests within American jurisdiction.
The sanctions are being prepared under the Global Magnitsky Act of 2016, which allows the US government to target individuals, companies or other entities involved in corruption or human-rights abuses anywhere in the world.
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Vice President Mike Pence told Fox News' "Sunday Morning Futures" that Brunson's release to house arrest "is just not good enough".
Family Research Council President Tony Perkins, who serves on the U.S. Commission on International Religious Freedom, said in a statement: "The president is not acting alone".
Washington and Ankara are North Atlantic Treaty Organisation allies.
Analysts say relations between the United States and Turkey have come under increasing strain in the past two years over the USA role in Syria and Turkey's stronger ties with Russian Federation. Turkey released him from prison on house arrest last week.
"President Trump concluded that these sanctions are the appropriate action", Pompeo said.
Turkey's foreign ministry said it had shared "necessary information" with the United States, but insisted the case should be left with its judiciary.
Though the sanctions designations on the two ministers were largely symbolic-and a far cry from broader sanctions on the financial sector the United States could deploy-they still sent the Turkish lira to a record low.