A 43-year-old man has been charged with the murder of a three-month-old boy.

The charge comes more than two years after the baby died in a house on the outskirts of Invercargill in January 2014.

The man, who is living in the Waikato, first appeared in the Hamilton District Court on Thursday when he was given interim name suppression and remanded to reappear in the High Court at Hamilton this morning.

Through acting duty solicitor Rob Weir, the man entered a not guilty plea and was remanded in custody by Justice Timothy Brewer to reappear in the Invercargill High Court on August 9.

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The man's name suppression will continue for the next four weeks.