Catalysis of the reaction: 5,10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH + H+ = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD+.
Statements about Methylenetetrahydrofolate-tRNA-(uracil-5-)-Methyltransferase (FADH2-Oxidizing) Activity