This paper gives a systematic study of the lowering operators acting on the $K$-$k$-Schur functions, motivated by the pivotal role played by the operators in the definition and study of Katalan functions. A lowering operator formula for closed $K$-$k$-Schur functions is obtained. As an application, a combinatorial proof is provided to a conjecture on closed $k$-Schur Katalan functions, posed by Blasiak, Morse and Seelinger, and recently proved by Ikeda, Iwao and Naito by a different method.