The charity picked up the award for its patient campaigning pack, which helps patients and carers to challenge NHS decisions if they are denied drugs.
Other winners were Stockport Council for the best big budget campaign and Lexia Media for best regional campaign. The PR on a shoestring award went to the Meningitis Research Foundation.
The awards were judged by past CIPR president Lionel Zetter, National Council for Voluntary Organisations CEO Stuart Hetherington and Fifth Estate chair Gill Dandy.
'PR and communications in the voluntary sector has come a long way since the Fifth Estate was set up,' said Dandy. 'The high level of comms expertise and professionalism in the not-for-profit sector is a testament to the hard work and dedication of those in the charity sector.'