Murphy won a Test cap for the Lions in the same country five years ago but wasn't part of the side beaten 19-13 by the Maori in the fourth game of that tour.
The 32-year-old follows in the footsteps of regular captain Brian O'Driscoll and stand-in skipper Paul O'Connell, with the former rested and the latter out injured.
Ireland have selected just one other Lion in their starting line up for their second match of the summer tour, with 2005 squad member Shane Horgan named on the right wing.
John Hayes, Donncha O'Callaghan, David Wallace, Ronan O'Gara and Rob Kearney are all among the replacements but the likes of fellow Lions O'Driscoll, Tommy Bowe and Gordon D'Arcy have been given the week off and Jamie Heaslip is suspended.
Munster-bound Johne Murphy starts on the left wing, with Jonathan Sexton named at outside-half alongside Eoin Reddan.
Gavin Duffy and Paddy Wallace combine in the centres, while Declan Kidney has opted for a new front-row combination in Marcus Horan, Tom Court and last week's debutant John Fogarty.
Ulster lock Dan Touhy, who scored a try just moments after coming on during Saturday's 66-28 defeat to the All Blacks, starts alongside his club colleague Ed O'Donoghue, with late call up Rhys Ruddock named on the blindside flank.
Ireland (vs New Zealand Maori, Rotorua, Friday 8.30am BST)
Geordan Murphy (captain), Shane Horgan, Gavin Duffy, Paddy Wallace, Johne Murphy, Jonathan Sexton, Eoin Reddan, Marcus Horan, John Fogarty, Tom Court, Ed O'Donoghue, Dan Tuohy, Rhys Ruddock, Niall Ronan, Chris Henry
Replacements: Sean Cronin, John Hayes, Donncha O'Callaghan, David Wallace, Peter Stringer, Ronan O'Gara, Rob Kearney
NB Bold denotes Lion