The Yorkshire batsman is all but guaranteed a starting spot in the subsequent Test series against the Black Caps but he is viewed as a potential England skipper of the future and the selectors are keen to give him leadership experience.
Ashley Giles, the senior side's limited-overs coach, will take charge of the team for the four-day match which starts at Grace Road on May 9.
Root will be leading out a strong Lions side which includes two other players who have genuine prospects of playing in the Test series - Yorkshire team-mate Jonny Bairstow and Durham seamer Graham Onions.
Ravi Bopara, Michael Carberry and James Taylor are the other Test-capped players to be named in the XI, while in Varun Chopra, Chris Woakes and Chris Wright there are also three players from Giles' former county Warwickshire.
Middlesex's in-form Toby Roland-Jones completes the pace attack, while Lancashire's Simon Kerrigan is the only frontline spinner.
National selector Geoff Miller said: "With a busy summer of Test cricket ahead, this fixture against New Zealand is an excellent opportunity for our players to show us that they are capable of representing England in the longer format of the game.
"Joe Root will lead the side in order to assist his development as a cricketer and provide him with valuable experience of captaincy against quality opposition."
Explaining the decision to involve Giles in the set-up, the ECB's managing director of cricket Hugh Morris added: "Our new limited-overs head coach Ashley Giles will be part of the Lions management team for this fixture and this will enable Ashley to closely monitor the performances of players who are competing for places in our T20 and ODI sides as well as the Test team."
England Lions team to face New Zealand: J Root (c), J Bairstow (wkt) (both Yorkshire), R Bopara (Essex), M Carberry (Hampshire), V Chopra (Warwickshire), S Kerrigan (Lancashire), G Onions (Durham), T Roland-Jones (Middlesex), J Taylor (Nottinghamshire), C Woakes, C Wright (both Warwickshire).
- Sports & Recreation
- Ashley Giles
- Jonny Bairstow
- Michael Carberry