Mr Justice Fancourt said Harry's amended case submitted earlier this year - which was reliant on the existence of the "secret agreement" - did not "reach the necessary threshold of plausibility and cogency".
He said emails between the Palace and NGN suggested there was "at some time an understanding" that the Royal Family's claims "would be addressed informally" at a late date, but the "vague and limited" evidence provided by Harry's lawyers did not amount to proof of Harry's specific claims.
From 2012, the judge ruled, Harry was "on notice" that he may have been hacked after finding out about the practice at the News of the World.
The judge said Harry "could easily" have had his lawyers investigate further, at which point a "much fuller picture would have emerged". The judge said the phone-hacking claim was therefore too late.