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(customize-set-variable case-fold-search  nil)

Or bind that variable (option) in your own command that is otherwise just a wrapper around query-replace. This has the advantage that it doesn't change the variable value for general use, outside of query-replacing.

See also variable case-replace, which controls case for the replacement text.

See also C-h f query-replace, where it says, for example:

Matching is independent of case if case-fold-search is non-nil and FROM-STRING has no uppercase letters. Replacement transfers the case pattern of the old text to the new text, if case-replace and case-fold-search are non-nil and FROM-STRING has no uppercase