@Jaspercohen said in Duex5 fan output problem:

M106 P7 I-1

This makes the pin available, now what do you want to do with it?
Is the pump intended to be switched on and off or run continuously?
Have you tested the pump yet with a direct 12v power source? Does it work?

At 1.6 amps for the pump you may come up against the current draw limit of the 12v regulator depending on what else you have connected to your fan ports.