Your fare is calculated based on how many kilometers you will travel. For further information on each type of ticket, please see the All Tickets page. To find your fare, you can go to Tokyo Metro Transfer Planner & Fare Calculation page.
Tokyo Metro Transfer Planner & Fare Calculationhttp://www.tokyometro.jp/en/ticket/search/index.html
(Even if you use a different route, you will only have to pay the fare for the cheapest route as long as you are only using Tokyo Metro lines.)