N-Phthaloylchitosan represents a key intermediate for the regioselective modification of chitosan in organic media. Chemoselective protection of primary alcohols on N-phthaloylchitosan was achieved with tert-butyldimethylsilyl (TBDMS) and tert-butyldiphenylsilyl (TBDPS) groups in imidazole/DMF and DMAP/pyridine. Influence of experimental conditions such as solvent, choice of base, stoichiometry, temperature, and time of reaction was studied regarding the degree of substitution (ds) of silyl groups. TBDMS groups allow higher ds than TBDPS groups. Higher reaction temperatures in different conditions led to lower ds and incomplete substitution. However, regioselective silylation of N-phthaloylchitosan was realized with ds up to 0.92 at room temperature. Silylated derivatives were characterized by elemental analysis, IR, and CP/MAS C-13 NMR spectroscopies.