Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron transport and thermoelectric response in the π-stacked structures by investigating five representative stacked molecular junctions. We found that a π-stacked system of two substituted anthracenes exhibits good thermopower and a high power factor, suggesting that increased conjugation can enhance the thermoelectric response. The fully eclipsed structure of quinhydrone exhibits a high power factor at the minimum energy structure and could thus be a better candidate in a thermoelectric device compared with the other π-stacked systems considered.