The Pakistan team failed to meet the official deadline for submitting the travel documents of its players.
The late invitation came after FIH had to officially withdraw Pakistan's invitation to the event.
"FIH regrets that Pakistan's men's junior team will not be able to take part in this year's Junior World Cup to be held in Uttar Pradesh even though they had officially qualified," a statement from FIH said.
"FIH's decision follows considerable discussions with the Pakistan Hockey Federation (PHF) and requests for confirmation that they had the necessary arrangements in place to be able to participate in the event," it said.
"Visas had been applied for after the official deadline and no accommodation was confirmed within the set deadlines. Despite a number of correspondence and reminders.
"The PHF was not able to show that their team would be able to travel to Lucknow for the event which begins in only a few days' time," the statement added.
"FIH has substantial contractual obligations to its partners to deliver a full number of matches at the forthcoming Junior Hockey World Cup for men," it added.
"With the event starting in only a few days' time, today (Tuesday) was the last possibility for FIH to ensure the quality of the event, with a full complement of 16 teams playing in Lucknow," the statement read.
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