This article presents a continuous capillary electrophoresis with laser-induced fluorescence (CE-LIF) following spectral studies of the noncovalent interactions between novel Squarylium Boronic Acid 4 (SQ-BA4) & Squarylium Diboronic Acid 2 (SQ-DBA2) squarylium dyes and human serum albumin (HSA). Two protocols were used wherein the on-column-labeling protocol was found to be more sensitive than the precolumn one by showing a better enhancement in the peak area of the HSA–dye complex besides lower limits of detection (LODs) for HSA. Also, stability studies were conducted with or without HSA using precolumn-labeling mode over one week exhibiting the superiority of SQ-BA4 to SQ-DBA2. Then, a mixture containing three model proteins, HSA, β-lactoglobulin B, and transferrin, was labeled on-column with both dyes and completely resolved by CE-LIF after optimization of several parameters. Both dyes provided lower LODs for HSA than those of β-lactoglobulin B and transferrin with higher sensitivities. In addition, the SQ-BA4 dye showed again greater sensitivities with all the three proteins than SQ-DBA2.