This paper proposes the rate control algorithm based on the S-JND (Saliency-Just Noticeable Difference) model for considering perceptual visual quality. The proposed rate control algorithm employs the S-JND model to simultaneously reflect human visual sensitivity and human visual attention for considering characteristics of human visual system. During allocating bits for CTU (Coding Tree Unit) level in a rate control, the bit allocation model calculates the S-JND threshold of each CTU in a picture. The threshold of each CTU is used for adaptively allocating a proper number of bits; thus, the proposed bit allocation model can improve perceptual visual quality. For performance evaluation of the proposed algorithm, the proposed algorithm was implemented on HM 16.9 and tested for sequences in Class B and Class C under the CTC (Common Test Condition) RA (Random Access), Low-delay B and Low-delay P case. Experimental results show that the proposed method reduces the bit-rate of 2.3%, and improves BD-PSNR of 0.07dB and bit-rate accuracy of 0.06% on average. We achieved MOS improvement of 0.03 with the proposed method, compared with the conventional method based on DSCQS (Double Stimulus Continuous Quality Scale).