The former vice-chairman stepped into the role in June last year following the resignation of Iain Dougan.
The 52-year-old served on the committee for over a decade across two stints, and also served as match secretary.
The Stair Park side’s current vice-chairman Robert H Rice confirmed the 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.”
Tributes have poured in from across Scottish football on social media.
A statement from fellow League Two side Stenhousemuir FC 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 FC 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.”
A post from Hamilton Accies official Twitter account added: “Condolences from all of us at Accies.
"Shaun was a popular figure throughout Scottish football and dedicated to his duties at Stranraer. RIP”
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.”
Colin Holden, president of the South of Scotland League, said: “Saddened to hear of the passing of Stranraer chairm an Shaun Niven.
"A well respected figure and great football guy. Will be missed by all who knew him. My condolences to his family at this difficult time.”