A continuous purification process can be beneficial to the purification of biologics due to its higher productivity and efficiency than a conventional batch purification process. However, regulatory issues and lack of established cases render deployment of the continuous process difficult in industrial settings. Here we report a case study for design and optimization of an advanced continuous process for purifying a low-titer enzyme as a model biologic. To convert a conventional batch process to an advanced continuous one in purification of biologics, conventional unit operations (UOs), including ultrafiltration/diafiltration (UF/DF) and batch chromatography, were replaced by advanced ones such as in-line dilution conditioning (IDC) and periodic counter-current chromatography (PCC). The UF/DF UO was changed to IDC UO to adjust pH and conductivity. The mixing ratio of the sample and the conditioning buffer in IDC was determined by experiments with three buffers. PCC was optimized with two variables, column height and sample loading residence time, as the delta pressure in the columns was less than 1.0 bar. A graph indicating the operating area was plotted to efficiently control the PCC. Although the sample volume increased in IDC, PCC had a complementary advantage in that purification was performed faster than batch chromatography. We observed at least 25% increase in economic advantage when the advanced continuous process was applied to purify a low-titer enzyme. We propose not only a continuous process with the substitution of UF/DF and batch chromatography with IDC and PCC but also a method to optimize PCC by plotting operating areas.