In 1949, who was the U.S. acting secretary of state on January 20th,
when George Marshall had resigned but Dean Acheson hadn't taken office
yet?

(It would normally be the undersecretary of state, but that person
also resigned on the 20th.)

Hello,

The answer to your question is Robert A. Lovett.

Source: "Lovett Says Soviet Must Act on Peace," New York Times, 20 Jan. 1949: 16.

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Perfect!