Only if you change line to a different operator, and there are transfer rebates.
Last time I lived in Tokyo, my hourlong commute that took me literally across the city (Yoyogi-uehara to Nezu) cost all of Y240 one way. This was on the cheaper side, but I'd wager the average commuter pays somewhere around Y500-600 (private railway plus metro), plus it's normally the employer that pays for the teikiken (commuter ticket) anyway.
