i have paid fee on behalf of my client on MCA website and charging the client one fee for the entire work done. Does GST apply on the entire value or should I charge MCA fee separately and reduce the GST charge on the Invoice
GST on reimbursements is not chargeable if service provided as a pure agent and amount paid was supposed to be paid by service receiver.
In this MCA fee falls within this criteria.
However you should have documents in place to prove this. You should have an agreement with your client specifying charges you will be paying on his behalf and he needs to reimburse them without any profit margin.
If you have this agreement in place or PO specifies this then you need not to charge GST on MCA fee paid by you.