Rate-compatible punctured LDPC codes have shown to perform well over a wide variety of code rates, both theoretically and practically. However it has been reported that the belief propagation (BP) decoding for these codes converges slower than for unpunctured codes. Layered BP algorithm is a modified BP algorithm that accelerates the decoding convergence by means of sequential scheduling of check node updates. In this letter, we propose an efficient scheduling of check node updates for rate-compatible punctured LDPC codes that performs well. We show that the convergence speed of the proposed scheduling outperforms conventional (random) scheduling and conventional, BP decoding. Performance improvements become more distinctive with the growing fraction of punctured bits.