The Young Bright Stars had been drawn into a strong Group C, where they were take Cameroon, Burkina Faso and Mali.
South Sudan has been disqualified from the U-17 Africa Cup of Nations for having over-aged players in the tournament, which got underway in Algeria on Saturday.
Of the 24 players who were in the residential camp preparing for their Group C opener against Cameroon, five of the footballers failed a Magnetic Resonance Imaging (MRI) age test.
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The Young Ocean Stars booked its ticket to Algiers after beating Uganda in the semi-final of the zonal play-offs.
It is a huge number given that it represents 20 percent of the players in camp preparing for the tournament, where they were also to face other continental giants Burkina Faso and Mali.
It is a huge blow for the Young Bright Stars, who were hoping to shine in Algeria, having earned the right to the tournament after reaching the final of the CECAFA regional qualifiers.
However, South Sudan Football Federation questioned their expulsion from the tournament, insisting that their tests had given all the players the clearance to feature in the continental tournament.
"We immediately wrote a complaint to the CAF medical committee, an official complaint against their decision attaching the MRI results we did in Juba , in accordance with Article 27.6 sub article (iii) of the U17 regulations. The complaint was rejected by the medical saying that their first and second readings remain the same,” the South Sudan Football Federation spokesperson Albino Kuek Deng said in a statement.
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Deng added that CAF conducted the MRI tests on Wednesday and results were released on Friday night which indicated they players were deemed ineligible to participate in the competition.
“We fully understand and respect the decision made by the competition's organizers, and we apologize to our fans, sponsors, and partners for any disappointment this may cause.
“South Sudan Football Association would like to emphasize that we have always been committed to fair play and sportsmanship. We have taken all the necessary steps to ensure that all our players meet the eligibility criteria set by the competition's regulations. However, due to unforeseen circumstances, some of our players were unable to participate in the competition,” adds another part of the statement.
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Should the Moroccan arrive at Stamford Bridge, he will have to compete with Reece James for first team place.
The U-17 Africa Cup of Nation got underway on Saturday with Somalia losing 2-0 to hosts Algeria in Group A opener.
Moslem Anatouf netted a brace for the hosts with his first goal coming in the 21st minute of the match courtesy of defensive lapse by the Young Ocean Stars before adding his second in the 51st minute after sliding through at the near post to connect to a corner on the volley.