The former Scotland international spent three years in charge of Championship side London and led them to The Qualifiers in each of the last two seasons.
Henderson, 38, has now joined the Wire who recently appointed Steve Price as head coach following Tony Smith's departure.
"I’m looking forward to bringing my experience and knowledge to a great group of players and playing my part in them reaching their potential and performing to our standards," Henderson told Warrington's official website.
"My experience at London has given me good grounding for this next step in my career. I’ve learnt a lot and thoroughly enjoyed my time at the Broncos, getting them back to a credible stage for them to be able to now kick on. However, I feel the time is right for me to move to the next level in this role."