If you need to set PRAGMA user_version use:
[self.db setUserVersion:yourUserVersion]; // yourUserVersion is of uint32_t type
To read current user_version user
[self.db userVersion]; // returned value is of uint32_t type
FMDB encapsulate it since 2013 so you don't have to deal with it yourself.
Documentation:
http://ccgus.github.io/fmdb/html/Categories/FMDatabase+FMDatabaseAdditions.html
PS: @HalR I think you can accept my answer as is it probably more useful for visitor searching for "how to set user_version PRAGMA" and it also solves your problem with neater solution as well.