The campaign, which is centred on the message 'life goes on', will be fronted by actress Gillian Bevan, whose character in Holby City, Gina Hope, was diagnosed with MND.
Holby City approached the MND Association six months ago. The charity failed to get the programme makers to drop the storyline in which the character will fly to a Swiss clinic to end her life, but did get significant concessions and ensured the disease was portrayed as accurately as possible.
However, BBC rules mean charities can rarely be named in drama programmes.
"The storyline has generated publicity for the cause, and it's up to us to turn that into publicity for the charity," said Richard Green, the charity's director of communications.