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I have a 3 pin motherboard plug in, and I plan to plug a splitter into to run 2 case fans from. The splitter is 3 pin female to two 4 pin male. The two fans I intend to plug in to the splitter are 3 pin. My local shop only carries these, otherwise I would buy the correct 3 pin adapter.

Most forums say you can plug a 3 pin into a 4 pin, but the fan will run 100% all the time. But will this still work?

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Yes, it'll still work. 3 Pin fans are voltage control (rough) while 4 pin is PWM Control (Fine), as you're outputting variable voltage, then going to 4 pins that you dont use, and only connecting the same three if it was all 3 pin.

They may run slightly slower than the rated speed due to there being two on one header, but normal control (like in your BIOS) should work just fine.

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