The “sensational” find was made between two rocks near a path above the village of Lungern, the canton announced on Thursday.
A group of archeologists from the Prospecting Working Group of Switzerland (AGP) began searching the area in the autumn of 2013 with students from the University of Basel.
The one-sided embossed coins date from the founding period of the Swiss confederation, begun by the three cantons of Uri, Schwyz and Unterwalden.
Were in a leather or cloth bag believed to have been either hidden by a traveller or simply lost between the years of 1280 and 1290.
Two-thirds of the coins were minted in the diocese of Basel, with the rest coming from Zurich and Schaffhausen, as well as Villingen in Germany and Strasbourg, France.
The origin of the coins can be traced to known images used, such as a depiction of a seated bishop for Basel or a ram jumping from a tower for Schaffhausen.
Discovering such coins is rare, said José Diaz Taberno, a researcher from the Swiss Inventory of Coin Finds (SICF), a group established in 1992 by the Swiss Academy of Humanities and Social Sciences.
Up to now only 17 coins of this type have been found in central Switzerland, and none until now were discovered in Obwalden.
Taberno in a statement said the value of the coins, around 10 shillings, in the 13th century is hard to assess.
But from information known about the city of Lucerne, in 1303 a sheep cost four shillings and a cow 12 shillings, while 1.7 litres of wine would have cost two and a half Pfennigs.
The coins were found near a path that was used by merchants, linking Lucerne to the Bernese Oberland and Italy, via the canton of Valais.
“We have a scientific treasure before us for which further investigation will be highly rewarding,” Taberno said.