Long-serving CEO Ivan Glasenberg, who had announced his long-expected departure in December, would retire on June 30.
The company said Glasenberg would seek re-election to the board at Glencore's AGM on April 29 for a further year.
Nagle will start on a base salary of US$1.8 million - part of a proposed total remuneration package of $10.4 million, Glencore's annual report revealed.
In other changes, Glencore said yesterday John Mack would retire from the board and not seek re-election at the AGM.
Meanwhile Tony Hayward is serving his final term as chairman and would leave by next year's AGM, Glencore said earlier this month.
Glencore closed 2.67% lower in London yesterday to 272p, remaining towards the top of a one-year range, valuing it about £36.2 billion (US$49.7 billion).