The 52-year-old long-standing committee member stepped into the role last May following the resignation of Iain Dougan.
Current Stair Park vice-chairman Robert H Rice confirmed the tragic news in a statement on the club website.
It read: “Stranraer Football Club is shocked and saddened by the death of its much-loved chairman, Shaun Niven.
“Shaun was a devoted football man and a great friend to all at Stair Park.
“Our thoughts are with Shaun’s family and friends at this awful time.”
Blues player-assistant manager Darryl Duffy added: “Absolutely devastated, actually can't believe it! Such an all round good guy and I will miss him.”
Niven was a popular figure throughout the game and clubs have been paying their respects.
A statement from fellow League Two side Stenhousemuir on Twitter read: “Such tragic news to hear this morning.
“Shaun was very much loved across the league and Scottish football.
“Sending our thoughts and love to Shaun’s family, friends and everyone at Stranraer FC during this difficult time.”
Livingston also posted a tribute, stating: “Shaun was a brilliant guy - he just ‘got’ Scottish football and what it meant to so many. An incredibly helpful and approachable man. A real, sad loss.
“Condolences from all at Livingston Football Club at this incredibly sad time.”
Motherwell chief executive Alan Burrows added his condolences.
He wrote: “My goodness, what awful and shocking news.
“The thoughts and deepest sympathies from all at Motherwell Football Club are with Shaun’s family, his friends and everyone at Stranraer FC.”