Cost. The cost of rebuilding a transmission at a shop varies. A good estimate cost for a transmission rebuild at a shop is between $1500 and $3000 as of 2009. Doing it yourself would likely be under $500, considering that all you have to pay for are the parts, not the labor.There are many variables. good estimate cost for a transmission rebuild at a shop is between $1500 and $3000 as of 2009. Doing it yourself would likely be under $500, considering that all you have to pay for are the parts, not the labor.