Last year owner Google imposed a blackout on music videos in March following a dispute over how much money it pays the PRS. The society collects royalties for composers and musicians.
The move resulted in the blocking of premium music videos supplied by record labels while content uploaded by artists or users will remain unblocked.
Under the PRS's new pricing structure digital sites will pay 0.0085p per track streamed online compared to the former rate of 0.22p. The new rate will apply for the next three years.
The said the decision was due to changes in the digital market since it last set its prices in 2007.
The decision appeared to be well received by YouTube. However, the site said it was still in discussions with the PRS over licensing and would not comment further.
PRS managing director of broadcast and online Andrew Shaw said: "We believe these new streaming rates will stimulate growth in the digital music market and will benefit our licensees and our members.
"As new entrants join the market and existing providers expand, music creators will reap the rewards by sharing in the success that their talent is generating. This is a good deal for music creators and for music lovers."
In April Billy Bragg, producer denouncing Google's dispute with the PRS as "cheapening" the music industry.