He directed the Francke Foundations and initiated approaches to medical practice, charitable treatment, and education at the University of Halle that influenced others internationally.

[2] A dissident evangelical reform movement, Pietism emphasized the practical application of theology and active charitable work.

[2] Juncker received free meals and lodging as part of an initiative, backed by a royal order, that collected funds for the support of students.

Juncker was a leader of Pietist medicine, influential in establishing approaches to medical practice, charitable treatment, and education at Halle.

Under Juncker's direction, the clinic provided free medical care to thousands of poor patients each year.

[16] Although other institutions were slow to model themselves on it,[16] Juncker's work at Halle inspired the establishment of clinics at Berlin, Göttingen, Jena, and Erfurt.

[1] In 1721 he published Conspectus chirurgiae, an alphabetical listing describing surgical and obstetrical instruments, bandages, and other medical equipment such as a vaginal cannula for treatment of uterine prolapse.

[21] Juncker was an energetic defender of the Halle physician Georg Ernst Stahl, who founded the phlogiston theory of combustion.

His treatment of Stahl's work on chemical composition and reaction was "critical and coherent", making it easier to understand and reaching a greater audience.

His first marriage was in 1707 to Charlotte Sophie the Countess of Waldeck and Pyrmont (28 January 1667 – 6 September 1723 in Halle), the daughter of Count Christian Ludwig.

[citation needed] He was succeeded in his position as professor of medicine at Halle by his son, Friedrich Christian Juncker.