The Jolly Roger wasn't flown by pirates all the time, and in fact pirate ships had many different flags, and usually flew false colours or no colours until they had their prey within sight. When the pirates' prey was within range, the Jolly Roger was raised, usually at the same time as a warning shot from a canon was fired.
The Jolly Roger is the name given to any of the many flags flown to identify a ship's crew as pirates. The flag usually identified as the Jolly Roger is the skull and crossbones, consisting of a skull above two long bones set in an x-mark arrangement on a black field. This design was used by several pirates, including Captains Edward England and John Taylor, and some Jolly Roger flags also include an hourglass, representing that the victims' time to surrender was running out.