A spokesperson for NGN called the ruling a “significant victory” that “substantially reduces the scope of his legal claim”.
The ruling was similar to one Fancourt made in May in a companion case brought by actor Hugh Grant, that also tossed out phone hacking charges.
Harry’s lawyer had argued he was prevented from bringing his case because of a “secret agreement” between the royal family and the newspapers that called for a settlement and apology. The deal, which the prince said was authorised by the late Queen Elizabeth II, would have prevented future litigation from the royals.
The publisher denied there was any secret agreement and Fancourt said Harry failed to produce evidence of such a deal.
Harry had said the rationale for the secret agreement was to avoid putting members of the royal family on the witness stand to recount embarrassing voicemails intercepted by reporters.
The case is one of three phone hacking lawsuits Harry has brought against British tabloid publishers in his battles with the press.
The decision comes less than two months after Harry testified in his lawsuit against the publishers of the Daily Mirror. He became the first senior member of the royal family to testify in a court in more than a century.