When it is time to pay the piper it is time to accept the consequences of a thoughtless or rash action. Or the phrase can mean that it is time to fulfill a responsibility or promise, usually after the fulfillment has been delayed already. Almost always the phrase is used with a pejorative connotation.
The phrase comes from the fable of the Pied Piper of Hamelin. According to the myth, a piper was hired to clear out the rats from the village of Hamelin. After he did so (by playing a song on his pipes), he was not paid for his work. His revenge for the lack of payment was to steal all the children of the town. The moral of the story was to pay the piper, or keep up your half of the bargain.
As a phrase, the verb is conjugated through all its forms.
A related phrase is he who pays the piper calls the tune. Somewhat self-explanatory. The phrase means that the one who is footing the bill gets to make the decisions. This is sometimes used to mean that the wealthy have all the power.