What is the Difference Between a System Fan and CPU Fan?

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

The fundamental difference between the system and the CPU fans is that the former is used for PC case/chassis ventilation, whereas the latter is used for CPU cooling.

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

In this article, I will explore the difference between the system and CPU fans in detail by looking at their headers on the motherboard.

What is a Header on a Motherboard?

First, let us get the technical jargon out of the way. A header is 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 a 3- or four-pin header for connecting fans.

They are tiny connectors with pins/terminals sticking out.

Also Read: What are USB Headers?

What is the Difference Between a System Fan and a CPU Fan?

To understand the difference between a system fan and a 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
Image: System Fan Header (Left), CPU Fan Header (Right) – The headers on the motherboard are clearly labeled.

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

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

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

CPU fan
Image: 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
Image: A high-performance CPU Fan by Noctua

The CPU fan’s physical look should help you better understand the difference between a System fan and a CPU fan.

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

2. System Fan Header

Also known as SYS_FAN and Chassis Fan, System Fan Header connects case fans to the motherboard. 

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

All the fans 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 three or more.

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

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

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

While you can split the fan header using the Y header splitter, ensure that the amperage of all the fans connected to a single title 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
Image: 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 four-pin. 3-pin System Fan Headers are used for DC fans, whereas the 4-pin System Fan Headers are used for PWM fans.

Both types of System Fan Headers provide power to the fans and monitoring and speed control.

3 Pin Header for DC Fans

3 Pin System Header - For DC Fans
Image: 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
Image: A Typical DC case fan with three pins.

4 Pin Header for DC Fans

4 pin system header watermarked
Image: 4 Pin System Fan Header

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

They are more expensive than DC fans but offer precise speed control and 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, and 200 mm.

The most common System Fan size is 120 mm.

noctua system fan
Image: 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
Image: Power Fan Header

This header is also very common on motherboards.

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

This fan header connects 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 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 usually 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 power up the extra radiator fans on a system with a liquid cooling solution.

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

Final Words

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

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


1. Can You Connect Case Fans to the CPU Fan Header?

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

This is not an ideal configuration but can be used if you seriously lack cooling and sufficient System Headers.

2. How Many System Fan Headers Can a Motherboard Have?

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

3. Can You Run two or More Fans from a Single Header?

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

I have written a detailed article on connecting Extra Fans To Motherboard.

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

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 a total 100% capacity all the time and will not adjust with temperature and workload, unlike the System and CPU Fan headers.

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