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Hi KK06, welcome to MySwissAlps!
Wheelchairs are certainly allowed. If you need help getting the wheelchair on and off board, then you can prompt a member of the railway staff before boarding in Grindelwald or Lauterbrunnen. In that case, I advice that you get there in time and explain your needs at the ticket desk or to another staff member. Quite some activities up at Jungfraujoch are wheelchair accessible as well.
General information can be found at http://www.myswissalps.com/ju ngfraujoch. If you’d like to reserve seats (not required, but it could be worth considering if you’re traveling in July/August, which are generally the busiest months), you can do so through http://www.myswissalps.com/ju ngfraujoch/tickets.