The cost of setting up an SMSF will differ depending on your needs as well as the type of company you use to establish your fund. Setup costs can vary from $1,000 or more than $10,000.Although a super cheap $1000 SMSF setup can seem very attractive, it is important to also consider the upgrade costs or any lock-in period which may apply.ur research a simple fund (without a Corporate Trustee) will cost you between $2,200-$3900. I generally not recommended to set up a SMSF without a Corporate Trustee.