El Badry was appointed as manager in the close-season, after departing Egyptian side Al Ahly, of Cairo.
The club announced the incident occurred after Al Ahly Tripoli's fixture with Al-Sowaihili on Saturday.
A statement read: "Our coach has been shot at his home after a match in the league against Al-Sowaihili that ended 1-1.
"El Badry is safe but in depression after what happened.
"Three men in a car shot our head coach. We spoke with the police and who have launched a full scale investigation."
El Badry has guided Al Ahly Tripoli to the top of the Lybian Premier League after taking seven points from their opening three matches.
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