The fossils of the genus stem from the White Water Member of the Blomidon Formation and were excavated in what is now Nova Scotia, Canada.

This not only makes Jupijkam one of the northernmost phytosaurs, but also one of the youngest, as these rocks date to the Late Triassic (Norian to Rhaetian).

After being found near the Bay of Fundy, the material was stabilized with the use of white plaster, which did not alter the shape of the fossil, before being acquired by the Yale Peabody Museum.

The genus name Jupijkam is derived from the horned serpent of Mi’kmaq mythology, which is also known as Jipijka’m, Chepechcalm and Tcipitckaam.

The species name derives from Latin words "palaeo" and "fluvialis", meaning "ancient" and "river" respectively, chosen to reflect the animal's likely habitat.

The fourth tooth, like in other parasuchids, is noticeably smaller than the first three and separated by all other subsequent premaxillary teeth by a short, toothless gap (diastema).

Following Jones and Butler, Jupijkam was recovered as a parasuchid phytosaur in a large polytomy alongside Colossosuchus, Angistorhinus, the clade formed by Volcanosuchus and Rutiodon as well as Leptosuchomorpha.

Utilizing the Datta and Ray dataset, Jupijkam was found to fall into the aforementioned clade formed by Rutiodon and Volcanosuchus.