An accurate description of anharmonic vibrational frequencies of polyatomic molecules is a challenging task. It requires an ab initio method to solve the vibrational Schrodinger equation along with extensive electronic structure calculations to generate the quartic potential energy surface (PES) in mass-weighted normal coordinates. The computation of such quartic PES is very expensive. Even for a medium-size molecule, highly accurate ab initio methods like CCSD, CCSD(T) become formidable. The DFT stands as valuable alternative in this case. In this work, we investigate the performances of several commonly used density functionals, namely, B3LYP, BLYP, B3LYPD, M06, M062x, PBE1PBE, B3P86, LC- $$\omega $$ PBE, X3LYP, B3PW91, and B97D for the evaluation of anharmonic vibrational frequencies of semi-rigid molecules. The quality of the results is assessed by the comparison with experimental values. To this end, we used a set of 19 molecules of various sizes (4–9 atoms). The vibrational coupled cluster method (VCCM) in bosonic representation is used to solve the vibrational structure problem. The hybrid functionals B3P86, B3LYP, B3PW91, PBE1PBE, and X3LYP found to give more accurate result of the fundamental frequencies than the other functionals. Our results show that the error in the BLYP and B97D calculation is due to the inadequate description of the harmonic force field. For the LC- $$\omega $$ PBE, M06, and M062x, the anharmonic force constants leads to the error. It is found that the comparative performances of the DFT functionals with VCCM are consistent with the second-order vibrational perturbation theory.