Henderson, who is yet to completely recover from a viral infection, was suspended for Thursday's 7-0 victory over Montenegro at Wembley as Gareth Southgate's side booked their place in the finals of the competition as Group A winners.
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His Liverpool team mate Gomez was booed by some fans when he entered as a substitute in that match, following a bust-up with Raheem Sterling on Monday, and misses the trip to Kosovo after sustaining a knee injury in training on Friday.
"Henderson arrived in camp with a viral infection that has not fully cleared," the FA said in a statement.
"Gomez sustained a knock in training and has not recovered sufficiently enough to travel.
"The pair now return to their club meaning the Three Lions will head to Pristina on Saturday with a 23-man squad."
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Henderson had given extra time to report for England duty and did not arrive in camp until Wednesday.
However, he was called upon as a senior member of the squad to mediate the dispute between Sterling and Gomez, with saw the former dropped from the team for Thursday's 7-0 win over Montenegro.
Henderson also sat the game out due to having picked up three yellow cards but Sterling is expected to come back into the starting line-up for Sunday's clash.
England have 18 points from seven games, while Kosovo are third in the group below Czech Republic with 11 points.