The fees structure in Thiagarajar College, Madurai varies based on the degree programme. Students need to pay the fee in instalments every academic year. The fees for B.A Tamil, B.A English and B.A Economics is Rs. 6159. For B.Sc Mathematics, B.Sc Physics,  B.Sc Botani, the fee is Rs. 7839, Rs. 6799, Rs. 6949 respectively. The fees for B.Sc Microbiology, B.Sc Computer Science, BBA and B.Com is Rs. 15949, Rs. 10249, Rs. 6309 and Rs. 6159 respectively. Rs. 5499 is for MA Tamil, MA English and MA Economics. For M.Sc Mathematics, M.Sc Physics, M.Sc Chemistry, M.Sc Botany, M.Sc Zoology, the fee is Rs. 6999, Rs. 6749, Rs. 7249, Rs. 6849 and Rs. 7249 respectively. The fees for M.Phil Tamil and M.Phil English is Rs. 3064 and Rs. 5114 for M.Phil Botany and M.Phil Zoology.