The cooler itself will since it's 160mm and the Urban S41 lists a 160mm limit.
However the NH-D15 is listed as 165mm with fans so you may want to consider that you may need to change the fans out if the 160mm limit is not including additional tolerance clearances. (for example the Urban S31 lists 145mm but fits 155mm , per hardocp) Edited by AlphaC - 4/28/17 at 11:18pm
The cooler and center fan will fit in the case. Front fan depends on RAM height.
A bigger problem is will it fit on your motheboard without blocking PCIe socket/s. D15 is 150mm wide so edge of finpack is 75mm center CPU toward PCIe sockets .. plus fan clips adding another couple mm.
If you could return your case I suggest doing so and getting something like the Define S for similar cost (. 233 x 465 x 533mm vs 516 x 220 x 520 mm).