Passengers can check-in online from 15 days to four hours before a flight.
The firm said the charge is a measure to encourage passengers to travel with the right documents.
Currently, passengers can have to pay a £40 "re-issue fee” if they fail to produce a boarding pass at the airport - potentially a problem for those without access to a printer.
Ryanair will also charge £100 to change the name on a booking online, or £150 over the phone.
According to the airline, the changes will translate to yearly savings of £44m – which will be passed on in cheaper fares.
Meanwhile, Ryanair said it made changes to its web site to make the online booking process less expensive and confusing, following demands from the European Commission. Concerns included the use of pre-ticked boxes that often led to the purchase of additional items such as insurance.
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