Hello, I thought I would bring this issue up here because I like the community. I have already reached out to the manufacturer, but they are not really helping. I just did a new build with an MSI z490 Unify and Noctua NH-D15 CPU cooler. I have the two fans for the cooler connected to Low Noise cables provided by the cooler, which are in-line and both go into a Y-splitter also provided by the cooler,  then finally into the CPU fan header. I have 3 other case fans plugged into other fan headers, and they are all working and reporting RPM. The MSI BIOS has a motherboard overview page that shows indication of things plugged into different areas. Every fan connection shows up except for the CPU fan header. For the CPU cooler setting in the BIOS I have already selected Tower Cooler.
 
I have updated the BIOS to the latest version, no change. The next step in my mind is to try taking out the Low Noise Cables, then the Y-Splitter, then trying some of the known working fans in the CPU fan header. I have looked around to try and see if there is just something I am missing on this, but I haven't been successful. If you all know something about this, I would be very happy to hear what you have to say. Thanks in advance!

This is the cooler . It lists what the cables are on that page. It comes with the Low Noise Cables (I think they cap the RPM to keep noise down) and the 4-pin Y-cable you mentioned. Its fine that they are connected in a Y-cable, they can run at the same speed without causing an issue. In fact, I don't know why I would need to control them at separate speeds based on their placement. I just worry that the PWM function probably isn't being used, so the fans are probably just running hard all the time for no reason.

Have you updated the bios?

bob16314
CPU Fan Mode set to PWM or Auto instead of DC in the BIOS -> Hardware Monitor section?

Never use one (L.N.A.) adaptor for both fans by putting it before the y-split cable per the Noctua NH-D15 .

Yes, CPU fan mode is PWM. Also, the connections are as follows:
 
Fan 1  >> LNA >> Y-Splitter << LNA << Fan 2
Then the single output of the Y splitter is connected to the CPU fan, per the Noctua instructions as you cited.

js_christie
I just built a new system yesterday with exact same motherboard and CPU cooler as you. Only difference is that I didn't bother with the LNA cables.
 
On my first boot up I also noticed that the mobo was reporting 0 RPM for the CPU fans, though I could see that they were both spinning. I then went into the hardware monitor section of the BIOS and started playing around with the fan speeds.  When I set the CPU fan speed to maximum, both CPU fans promptly sped up and the mobo reported around 1490 RPM (the fans max at 1500 so that should be correct).
 
So it seems that the mobo is able to control and read the RPM of the CPU fans just fine, even with the Y split cable, but at normal low idle it's registering as 0 RPM.
 

Thank you for telling me that. I'll do some testing myself with that in mind. They makes me feel a whole lot better. I may take out the LNA cables too.

js_christie
So can further confirm that fans properly spin up under load. Running CPU stress tests, the fans speed up as the heat increases and properly show their RPM once they cross the initial idle threshold. Still seems strange they register as 0 RPM at low speed, but they are working.

Thank you for your help! You are amazing.