It's an injury which requires surgery and leaves the youngster's prospects of featuring in Russia next summer hanging by a thread.
Indeed, Onyekuru looks primed to join the unhappy list of Nigeria players who have missed world football's global showpiece due to injury.
In this feature, KweséESPN remembers four Super Eagles who were denied a shot at the grandest stage of all after fitness misfortunes.
Ike Shorunmu: The Super Eagles' preparations for France '98 were hit by a massive setback on the eve of the tournament with the news of the arm injury sustained by Ike Shorunmu.
The talented goalkeeper, then on the books of FC Zurich, was set to be the Eagles' first-choice goalkeeper following his superlative performances -- for club and country -- in the months leading to the tournament.
Notably, he excelled in a 1-0 loss to Germany, an international friendly in which he pulled off several spectacular saves.
With Nigeria conceding a total of 12 goals in friendly defeats to Yugoslavia, Grasshoppers and Netherlands in the aftermath of Shorunmu's broken arm, Peter Rufai was handed a late recall to the squad, a last-ditch move which ended with a disappointing 4-1 second round defeat to Denmark.
Yakubu Aiyegbeni: A series of events at the 2002 African Nations Cup final in Mali led to the Super Eagles team being disbanded ahead of the World Cup in South Korea and Japan.
Yakubu had contributed immensely to the team's qualification, notably against Sudan in Omdurman, scoring a brace and delivering a Man-of-The-Match performance. However, he was controversially left out of the World Cup party on account of an eye surgery while on the books of Maccabi Haifa.
It was a difficult decision to comprehend, considering the player's goal had secured third place for Nigeria at the Nations Cup earlier in the year. Similarly, he was back playing at his club before the season's end.
His potency in front of goal was sorely missed in an eventual group-stage exit, with Nigeria drawing a blank against England Argentina.
Ike Uche was primed to be one of the star players at the 2010 FIFA World Cup in South Africa, the first time the global football tournament was held on African soil, after scoring four during qualification.
A ruptured cruciate ligament in his left knee, suffered while featuring in a Spanish top flight game for Real Zaragoza in September 2009, denied him a maiden World Cup showing.
Despite returning to fitness a month before the announcement of the final World Cup squad, his 45-minute performance in an international friendly against Saudi Arabia convinced coach Lars Lagerback that the fan favourite was not mentally and physically ready for the tournament.
John Obi Mikel: What seemed like a minor injury sustained in a Premier League game against Tottenham Hotspur ultimately cost Mikel a spot at the 2010 World Cup, with the midfielder requiring unexpected surgery.
"We have dropped Mikel from the World Cup after he told the team he did not want to put his career at risk as his knee injury has yet to fully heal after a recent surgery," team co-ordinator Emmanuel Attah told journalists, as per the Daily Mail.
Unlike Uche, however, Mikel ultimately made up for lost time. He represented Nigeria at the 2014 showpiece, and appears primed to lead the Super Eagles to Russia next summer.