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Replacing the engine in a 2006 4runner can be quite expensive, costing around $3000 for a used or rebuilt engine. It's unlikely that you'll be able to find a new one, and if you do, it will be significantly more expensive. Additionally, the labor for removing and replacing the engine will cost an additional $1000 to $1500 on top of the engine cost. This process will likely take at least two days, so be prepared to be without your car for a while. Considering the age of the vehicle, it may be more practical to explore getting a new model rather than investing in repairing the current one.
It varies depending on your location. I am acquainted with a person who undertook a JDM project entirely on his own, which cost around $3,000 to $4,000. Currently, I am working on a similar project for a 1998 model, also on my own, and utilizing a remanufactured 5vzfe engine. The total cost is estimated to be closer to $5,000 to $6,000 after factoring in the replacement of additional essential components like the clutch, fan bracket, and hoses. A nearby garage advised that labor costs alone would amount to around $3,000.
On average, you can anticipate spending approximately $3,000 for parts if you need to replace the engine in a 2006 Toyota 4Runner. Additionally, labor expenses will be an additional $1,000 to $1,500.