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This price will vary depending on the labor rate for your area and the quality of parts used, but I normally see around $1,500-$2,000 to rebuild an automatic transmission in your car.
I would however like to make a suggestion. Before having an independent repair center rebuild your transmission, I recommend to my customers to use a Genuine Honda remanufactured trans. They carry a 3 year/36,000 mile warranty backed by Honda (very important to me) and we have installed several of them and they work great. Retail price is around $2000 + labor and I know that is more money....but considering it is built and backed by Honda....I personally feel it is worth the difference.
Used transmissions for the 01-05 Civic's are hard to find in good condition as they are very troublesome. My shop has changed at least 25 of them.
I hope this helps you out, but if you need anything else, please let me know.
I understand completely. The 01-05 Civic engines are almost bullet proof, but the transmissions have proved to be quite troublesome. The first thing I would ask is how long is the warranty? And you might want to find out how long the shop has been in business....because the warranty only lasts as long as the shop does...it would just help to know they were not a "freshly opened" business. If a shop has been around a few years...it would make me feel more comfortable.
Also, you want to clarify that the transmission is getting a complete rebuild...not just a repair for whatever is wrong with it as other parts inside the trans. might go bad in the near future. I would just be sure that for this price they are going to replace anything that normally wears out (e.g., clutches, bearings, seals, gaskets, solenoids)