It was founded at Guajataka Scout Reservation, next to Guajataca Lake in San Sebastián, between April 10–15, 1954 by Luis Matías Ferrer and Dr. Frank H.

The Lodge adopted the Three-Point Taíno Cemí as its totem and Yukiyú as its name, the latter which was eventually changed to Yokahu as a proposition by Dr. Ricardo Alegría.

With the necessary requirements in hand provided by the OA National Office, the council tasked the founding of the Order of the Arrow in Puerto Rico to its executive Luis Matías Ferrer in 1954.

Having no knowledge of the organization, he sought the help of Dr. Frank H. Wadsworth, an American forester who had been inducted in the Order of the Arrow during his youth in the United States, and was also the only Arrowman in Puerto Rico at the time.

Because of his role in the first Ordeal ceremony, Wadsworth has been often recognized as the Yokahu Lodge's main, or sometimes sole, founder throughout its history with not enough credit given to Luis Matías Ferrer.

In the beginning, the Lodge translated the ceremony scripts from English to Spanish and used Native American regalia, but decided later to slightly modify the ceremonies by assimilating the Taíno heritage with the Lenni Lennape culture, incorporating Taíno-based regalia and adapting the scripts to the Taíno culture.

More or fewer chapters were created or merged with others to adapt to changes in their membership and in the national and local regulations of Scouting America[a] and the Order of the Arrow.

Halfway through the year, the Lodge celebrates its high adventure activity between August and September, in order to challenge each Arrowmen's outdoor skills.

In October, the Lodge celebrates its Guateke (from the Taíno language, meaning gathering), a fellowship event in which chapters participate in various competitions such as ceremony, regalia, dialogue, sports, triathlon and trivia; the highlight of the Guateke is the youth nominations for the positions of the Lodge Executive Board during the Fall Assembly.

The 2008 NE-2A Section Conclave took place at Guajataka Scout Reservation, marking the first time that the Yokahu Lodge hosted such event and the first to be held outside the United States.

Yokahu hosted the NE-5A Section Conclave in August 2016 at Guajataka Scout Reservation for the second time in its Lodge history.

In January 2012, the Lodge launched their official Facebook[3] and Twitter[4] accounts, integrating the era of social media to their communications and establishing efficient interactions with their Arrowmen.

The publication, social platforms and email are all managed between the chairman of the communications committee and the Lodge secretary, with assistance from the adult advisers.