What is the Difference Between System Fan and CPU Fan?

All motherboards have different type of fan headers that serve different purposes. The two most common fan headers that people confuse between are System and CPU Fan Headers. Which begs the question: what is the difference between System Fan and CPU fan?

Basically, the fundamental difference between the System and the CPU fans is that the former is used for PC case/chassis ventilation where as the latter is used for the CPU cooling.

Knowing the difference between the two is essential for installing ventilation for your desktop PC correctly.

In this article I will explore the difference between System Fan and the CPU Fan in details by particularly looking at their headers on the motherboard.

What is a Header on a Motherboard?

First things first, let us get the technical jargon out of the way. A header is basically another name for a connector on a motherboard. 

There are headers for different purposes i.e

  • Fans
  • USB ports
  • Audio
  • PC Case front Led lights
  • PC Case power and restart button etc.

Also Read: What is Front Panel Header?

What is a Fan Header?

A fan header is basically a 3 pin or a 4 pin header for, well, connecting fans to.

They are very small connectors with pins/terminals sticking out.

Also Read: What are USB Headers?

What is the Difference Between System Fan and CPU Fan?

To understand the difference between System Fan and CPU Fan, you must understand the different types of fan headers.

There are essentially four types of fan headers that you can find on your motherboard:

  1. CPU FAN Header
  2. System Fan Header
  3. Power Fan Header
  4. CPU OPT Header

1. CPU Fan Header

fan headers on motherboard labelled watermarked
System Fan Header (Left), CPU Fan Header (Right) – The headers on the motherboard are clearly labelled.

Also known as and abbreviated as CPU_FAN, as the name suggests, this header is used for connecting the power pin of the CPU cooling fan. It comprises typically of 4 pins.

Basically, to power up the CPU cooling fan, you would use this header.

Like other fan headers, the CPU Fan header also typically has a maximum amperage rating of 1A.

CPU fan
CPU cooling fan is placed on top of the CPU. The power connector of this cooling fan connects to the CPU FAN Header.

A motherboard almost always has only a single CPU Fan header.

Note that your PC will NOT start if the CPU FAN header is not connected to the cooling fan!

What Does CPU Fan Look Like?

CPU fan
A high performance CPU Fan by Noctua

The physical look of the CPU fan should help you understand what is the difference between System fan and CPU fan better. 

CPU fans are designed to dissipate heat from the CPU. The sit right on top of the CPU have harnesses that keep them in their place. 

2. System Fan Header

Also known as SYS_FAN, and Chassis Fan, System Fan Header is used for connecting case fans to the motherboard. 

It provides the connected fans with voltage control, speed control and monitoring capability.

Basically, all the fans that you install on the PC case should ideally have their power connected to the System Fan Headers.

A motherboard can have multiple System Fan Headers. Some have 2 others can have 3 or more.

Like all fan headers, the System Fan Headers also have a typical amperage of 1 amp.

Make Sure to Not Exceed the Amperage Rating of the Fan Header

It should be noted again, that the fan headers have a rating of 1 amps.

While you can split the fan header using the Y header splitter, make sure that amperage of all the fans connected to a single header does not exceed 1 amp.

Ideally, the total amperage of all the fans connected to a single System Header should be around 0.75A (or 75% of the total amp rating of the header). 

fan header splitter 2 way
A Y fan header splitter is the easiest way to connect multiple fans to a single fan header on your motherboard.

3 Pin vs 4 Pin System Header

There are two types of System Fan Headers: 3 pin and 4 pin. 3 pin System Fan Headers are used for DC fans whereas the 4 pin System Fan Headers are used for PWM fans.

Both type of System Fan Headers do provide power to the fans and also provide monitoring and speed control.

3 Pin Header for DC Fans

3 Pin System Header - For DC Fans
3 Pin System Header – For DC Fans

As mentioned earlier, the 3 pin System Fan Header is used for DC fans.

DC fans have been around for longer. They are cheaper and offer inferior speed control.

System fan header 3 pin
A Typical DC case fan with 3 pins.

4 Pin Header for DC Fans

4 pin system header watermarked
4 Pin System Fan Header

4 Pin System Fan Header are used for installing PWM fans.

They are more expensive compared to DC fans, but offer precise speed control and also generate lower noise. 

What Does System Fan Look Like?

System Fans or Chassis Fans, come in various sizes defined by their diameter in mm. i.e 92 mm, 120 mm, 140 mm, 200 mm. 

The most common System Fan size is 120 mm.

noctua system fan
A 120 mm System/Case fan by Noctua

System/Case fans can also be found in hub configuration whereby you can find dual or triple fans in a single frame.

3. Power Fan Header 

What is the Difference Between System Fan and CPU Fan
Power Fan Header

This header is also very common on motherboards.

In addition to understanding what is the different between System Fan and CPU Fan header, it is also worth understanding what the Power FAN header is for.

This fan header is used to connect the power supply fan to it for monitoring purposes. Not all power supply units have the appropriate wires or the feature to support the Power Fan Header. 

The Power Fan Header CAN ALSO be used to add more case fans. However, unlike the System Fan and the CPU Fan Headers, the Power Fan Header does not provide any speed control.

In other words, the fans on the case will NOT throttle depending upon the temperature the system is being run at. 

The fans connected to Power Fan Header will be ON and working at 100% capacity all the time. 

4. CPU OPT FAN Header

CPU OPT stands for CPU OPTIONAL Header. 

Often abbreviated as CPU_OPT, this header is often found in conjunction with the CPU_FAN Header on select high end motherboards. 

It is often used for systems featuring CPU coolers with two fans. The CPU_OPT can be used for the second fan.

It can also be used for powering up the extra radiator fans on a system with liquid cooling solution.

Also Read: How to Monitor CPU and GPU Temp While Gaming?


Can You Connect Case Fans to CPU Fan Header?

Yes, you most certainly can. You can split the single CPU Fan Header using a Y splitter as shown above for connecting your CPU cooling fan and your case fan to the CPU FAN Header.

This is not an ideal configuration to have, but can be used in case if your seriously lack cooling and sufficient System Headers.

How Many System Fan Headers Can a Motherboard Have?

A mother can have multiple System Fan Headers. Some have two others have three or more.

Can You Run 2 or More Fans from a Single Header?

Yes, you most certainly can. Most fans are rated at about 0.10-0.30 amps so you can certainly use multiple CPU off from a single header.

I have written an article on this topic in detail: How to Connect Extra Fans To Motherboard?

Can PC Case Fans be Plugged Into a Power Fan Header?

Yes, as mentioned earlier, you can connect the case fans to the Power Fan Header. However, Power Fan Header provides no speed control.

As such the fans connected to this header will run at full 100% capacity all the time and will not adjust with temperature and workload unlike the System and CPU Fan headers.

Also Read:

Final Words

Here I talked comprehensively about what is the differences between System Fan and CPU Fan and their headers. 

Different fan headers have different uses and knowing what each is for will help you building an efficient cooling system for your PC. 

Photo of author


Atif Qazi
Atif Qazi is the founder of PCGuide101. He is a digital nomad who loves everything PC. He is a PC builder, tech enthusiast, engineer, and a lover of single player lore-rich RPG games.

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