Huber was born on July 15, 1865, in Zürich-Riesbach, Switzerland the son of Peter Emil and Anna Marie (née Werdmüller).
After training as a mechanical engineer at the ETH Zurich (Swiss Federal Institute of Technology at Zürich) and spending some years in America, Huber took over the management of the Maschinenfabrik Oerlikon, founded by his father Peter Emil Huber-Werdmüller, near Zürich, Switzerland.
In 1904, he electrified the Seebach-Wettingen line with high-voltage alternating current (15,000 volts) at low frequency (15 Hertz).
In 1925, Emil Huber-Stockar received an honorary doctorate from the ETH Zurich for his achievements.
In 1895, Emil married Marie Helena Stockar, daughter of Hans Julius, a lawyer.