A series of 2,7-dipyridylfluorene derivatives have been synthesized with different substituents (2H, 2Me, 2OMe, 2CF3, and O) at the C(9) position. Experimental measurements on gold|single-molecule|gold junctions, using a modified scanning tunneling microscope-break-junction technique, show that the C(9) substituent has little effect on the conductance, although there is a more significant influence on the thermopower, with the Seebeck coefficient varying by a factor of 1.65 within the series. The combined experimental and computational study, using density functional theory calculations, provides insights into the interplay of conductance and thermopower in single-molecule junctions and is a guide for new strategies for thermopower modulation in single-molecule junctions.