After campaigning as a strong supporter of the use of ethanol and other biofuels in the nation’s gasoline supply, President-elect Donald Trump has chosen a forceful adversary of those federal requirements to implement them.

Mr. Trump’s pick to run the Environmental Protection Agency, Oklahoma Attorney General Scott Pruitt, has called the ethanol mandate “unworkable” and filed a legal brief in 2013 backing a lawsuit challenging it. Mr. Trump during his transition also has sought advice from other critics of the program, many...