As per documentation:
Salesforce does not allow direct field to field comparison in SOQL query.
To achieve this you may create a formula field that will compare fields and return a value (like true or false) which you may use in a WHERE clause.
So for the above query, you could create a formula field on User object with return type Text e.g. NameCompare, with the formula
IF(User.FirstName != User.LastName, 'true', 'false')
Now our query will be:
List<User> Users = [SELECT id, name FROM User where NameCompare= 'true'];
Following idea has been posted on ideaexchange portal for allowing field-to-field comparison in SOQL:
You could simplify/clean up the above approach by using a checkbox formula:
User.FirstName != User.LastName
Which would change the query to:
List<User> lstUser = [SELECT Id, Name FROM User WHERE NameCompare = true];