The mobile phone firm chose the charity as it felt it could use its position as a communications company to help those with communication problems.
Vodafone will promote the NAS to its 13m customers, encouraging them to donate either regularly or a one-off payment.
The mobile operator claims to be the first to enable customers to make donations via their phone bill by texting a shortcode. A dedicated website will also be set up, with Vodafone pledging to match all customer donations received.
Later in the year Vodafone will promote the tie-up through a TV advertising campaign.
The £6m raised will go toward three projects for the NAS, including a 24-hour support programme offering help and advice on autism by phone or online.
Mark Bond, Vodafone UK's director of business marketing, is overseeing the partnership.