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I have a project in which I need to drive 48VDC 90W fan and control it using it's PWM line.

I've found a number of resources including this, which seems to state that I can directly control the fan using a PWM pin from my microcontroller.

My concern however, is due to the much higher voltage of the fan, I feel like it would be unsafe for the fan to share a common ground with the microcontroller (5v).

What should one do to control such a setup safely?

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Without any special circumstances (such as large currents in the shared ground) sharing a ground with a high voltage is no problem, we do it all the time: we share the ground (literally) with all kinds of high-voltage power lines.

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  • \$\begingroup\$ The linked question grounds the fan's voltage to the Arduino's ground pin, this isn't unsafe at all? \$\endgroup\$
    – keag
    Commented Sep 14, 2015 at 17:35
  • \$\begingroup\$ voltage is a concept that only makes sense relative to something else: the correct name would be voltage difference. Without complicating circumstances you can connect one lead of a voltage source any way you want. The trouble (or fun) can only start you also connect the second lead. \$\endgroup\$
    – Wouter van Ooijen
    Commented Sep 14, 2015 at 17:44
  • \$\begingroup\$ I was concerned, but once I actually had my circuit laid out, it made sense why this wouldn't be a problem. Thanks for the help! \$\endgroup\$
    – keag
    Commented Sep 14, 2015 at 19:36
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There shouldn't be a problem connecting the two grounds together. In fact, you have to do so in order for the PWM signal to work properly. You could use optoisolation, but your system is small enough that it doesn't really gain you anything.

What you could do is wire up the system in a way that keeps the PWM ground stable. This means having the return current from the fan and the return current from the PWM go through separate wires and/or PCB traces:

schematic

simulate this circuit – Schematic created using CircuitLab

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