He worked in the canton Appenzell and made livings as a Carpenter. Afterwards he was trained in Basel as a Evangelist deacon (Krankenpfleger). In 1899 he traveled to Urfa in Turkey, where he found out it was actually a effective place. He continued to form medicine up to becoming a independent operating surgeon, and later he got married in 1905 to Elizabeth Bende, daughter of a Christian Missionary and granddaughter of a Ethiopian princess.
1915-1917 Künzler became a eye-witness of the genocide aimed at the Armenians , he writes in 1921 in his book with the title “in the country of the blood and the tears”. Under mortal danger it, where it could, helped provided for thousands of Armenian orphans and resumed the hospital enterprise in Urfa.
A Swiss pharmacist who had remained in Turkey serving the sick and wounded, non-Muslims and Muslims alike, in a hospital in Urfa who documented accounts of massacres of various Armenian labor battalion companies. 
In October 1922 he closed his hospital he worked in and pulled his family after Ghazier in close proximity to Beirut, where later he opens a center for orphans. Later he establishes a settlement for Armenian widows in Beirut and in Azounieh a lung sanatorium.
Jakob Kunzler observed in August 1915: "two Turkish officials who appeared in Urfa. The rumor was that they hurried out in order to drive forward the extermination of the Armenian people with all their might, and they had the sanction of the highest state authority for doing so. They ordered on this basis, scarcely the moment they arrived in Urfa, the killing of all gathered prisoners. 'Why should we feed them any longer?' they said."
Prizes and honors
- 1947 award by the University of Basel
- 1959 Gedenkstein in Hundwil
- 1971 earnings/service medals of the Lebanese government
- 1971 Gedenkstein in Hundwil and roller living (1971).
- 1929: In the country of the blood and the tears
- 1959: Köbi of the stopgaps in the service of the life
- Turkish Atrocities: Statements of American Missionaries on the Destruction of Christian ... - Page 109
- The Treatment of Armenians in the Ottoman Empire, 1915-1916: Documents Presented to Viscount ... - Page 538 by Arnold Joseph Toynbee
- International Affirmations of the Armenian Genocide – from International Organisations, p.7
- America and the Armenian Genocide of 1915 - Page 66 by Jay Murray Winter
- Jako Kunzler, Dreissig, Jahre Dienst am Orient, (Basel: Emil Birkhauser and Cie, 1933), p.53