According to 
http://www.powersportspro.com/pages/parts/viewbybrand/2/Yamaha.aspx it will work.
Look up your part # once, then enter it in their "Quick Part Lookup" and it'll list all models that use it.
12200-37E01      
RM250 (1996)
Assembly: CRANKSHAFT
CRANKSHAFT ASSY MODEL T/V (SKU: 12200-37E01) (Supersede: 12200-37E40)   1   $458.66          
12200-37E01      
RM250 (1997)
Assembly: CRANKSHAFT
CRANKSHAFT ASSY MODEL T/V (SKU: 12200-37E01) (Supersede: 12200-37E40)   1   $458.66          
12200-37E01      
RM250 (1998)
Assembly: CRANKSHAFT
CRANKSHAFT ASSY MODEL T/V (SKU: 12200-37E01) (Supersede: 12200-37E40)   1   $458.66          
12200-37E01      
RM250 (1999)
Assembly: CRANKSHAFT
CRANKSHAFT ASSY MODEL T/V (SKU: 12200-37E01) (Supersede: 12200-37E40)   1   $458.66          
12200-37E01      
RM250 (2000)
Assembly: CRANKSHAFT
CRANKSHAFT ASSY MODEL T/V (SKU: 12200-37E01) (Supersede: 12200-37E40)   1   $458.66