The former Rangers captain takes over from Jim Duffy at the SPFL League 2 side, who left for his old club Morton last month, and will have the well-travelled Malky Thomson serving as his assistant.
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Ferguson, 36, spent the second half of last season in a caretaker-manager role at Blackpool steering the club to safety in the Championship.
"We are delighted that Barry has committed himself to taking Clyde forward as player-coach," said John Alexander, the club chairman.
"He won us over with his vision for developing our squad and commitment to building on our existing youth policy as he establishes himself as a manager in the Scottish game."