When a hotend reaches a certain temperature, the fan will turn on to keep it from overheating, which would otherwise cause a jam. Unfortunately, most fans are really loud, but some manufacturers are producing fans that are almost silent. Noctua fans are one of the most famous, not just when it comes to 3D printers.
Replacing the hotend fan
The stock fan on a Prusa is 30mm, but Noctua doesn't sell anything smaller than 40mm, so you'll have to buy that one. Just be careful to buy one with the correct voltage. Most printers use 12V for their fans, but there are some exceptions (like the Creality Ender 3) which use 24V for the fans as well.
Here's a link for the Noctua 40mm 12V fan.
Many fans come with 3 wires, one of which is used as a signal wire that reports actual RPM's back to the device. On the majority of printers, the yellow signal wire is not used, so you can cut it away. The Original Prusa Mk3 does use the 3 wire configuration though, so be sure to double check your printer before you cut away anything.
I highly recommend that you use Dupont connectors (standard plugs that you see on computers and electronics). Fans used for 3D printing fail quite often and it's very likely that you'll have to replace yours in the future. Having connectors that you can just plug new fans in to will save you tons of time and frustrations down the road.
I've made a separate video on Dupont connectors and 5 other ways of connecting wires, so check it out if you want to find out more.
Because Noctua fan is usually larger than the stock fan, you'll have to print an adapter for it. While you can use PLA (the fan should be far away from the hotend), I highly suggest that you use PETG or ABS instead.
Before you mount the adapter, start a thread in each hole first. It's much easier to do it now and will make your life a lot easier when you'll have to attach the fan.
Next, carefully remove the old fan. Take it slow, other nearby wires for the heater and thermistor are very fragile.
Cut away the wires as close to the old fan as possible. It might be difficult to attach the new fan if you don't have enough of the wire left.
Again, I highly recommend that you use the Dupont connectors. Use the female connectors for the wires of the old fan.
Continue by attaching the adapter for the new fan. Don't cut away or shorten the wires of the new fan, we don't know the exact length yet.
Now attach the fan as well.
With the adapter and fan securely in place, we can cut away the fan wires now. You should leave about 5cm of extra length and cut away the rest.
Attach the male Dupont connector similarly as you did before and then connect the two cables.
Wrap electrical tape around the connectors just for good measure. The constant movement and vibrations of the hotend might loosen the connectors apart over time.
Now it's time for some cable management. Route the new cables close against the hotend, other cables, possibly the bowden tube if your printer has one. Basically, ensure that the new cable won't hit any part of the printer while the hotend is moving. It's very important to check that the new wires are not hitting anything, especially the frame. Take a look from multiple sides. I've also applied just a bit of glue on the new wires to really hold them in place.
You can now power on the printer and check if the fan is working. On some printers, you'll have to heat the nozzle to about 50°C before the fan will turn on. You can do a self-test on Prusa so that you don't have to heat up the nozzle and then just reset the printer when the fan is working.
Replacing the part cooling fan
For the part cooling fan, you will need at least the 60mm version if you want to achieve the same airflow as with the stock radial fan.
Same as before, be sure to get the 12V or the 24V version depending on your printer.
You will also need to print an adapter first. There are multiple designs available on Thingiverse, I've decided to go with this one by Crunch3D.
Everything else is basically done in the same way as before. Cut away the old wires, attach the adapter, create Dupont connectors and plug everything back together.
I suggest you print a torture test like this one. Pay special attention to overhangs and bridging. The new adapter might be restricting too much airflow or there might be something wrong with the fan. Issues like this will be most noticeable with overhangs, where good cooling is critical.
Amazon affiliate links
If you wish to buy any of the items mentioned here, you can use my Amazon affiliate links below. As an Amazon Associate I earn from qualifying purchases.