1 The cost of an MRI machine depends upon the size of the machine. 2  Usually, you can expect to pay anywhere from $500,000 to an upwards of $1,000,000 for an MRI machine. 3  In certain cases, the MRI machine can cost $10,000,000. For a typical installation for an MRI System, expect to spend between $40,000 and $80,000. 2  Also, inquire about ongoing service costs. 3  Look for specialized engineers that can properly handle MRI’s. 4  These include reliable, operation and maintenance costs.