(how) can I use 250v fuse in a 9v circuit?
You can use them at lower voltages (they will be safe) but you may see excessive voltage drop for your application. 

You did not specify whether your proposed application is AC or DC. In general you can use AC-rated fuses for DC voltages beyond 12V (maybe up to 32V), but read the datasheets. High voltage DC (such as 125VDC) is a horse of a different color- generally not safe at all. 

This also assumes that your fault current cannot exceed the interrupting capacity of the fuse. For the small glass fuse it's 35A.

For example, a bog-standard 100mA 5x20mm glass fuse from Bel drops about 1.63V so you'll lose more than half your voltage at full current. At 1.6V across them they may never open at all. 

This is not a consequence of the fuses being rated for high voltage- it's because they actually require enough power (mW) to heat the fuse element to melting. There are one-time (even SMT one-time) and self-resetting 'fuses' that may be more appropriate for low voltage but there will always be some voltage drop.