As far back as the 19th century, a cookie very similar in appearance to the modern fortune cookie was made in Kyoto, Japan; and there is a Japanese temple tradition of random fortunes, called omikuji. The Japanese version of the cookie differs in several ways: they are a little bit larger; are made of darker dough; and their batter contains sesame and miso rather than vanilla and butter. They contain a fortune; however, the small slip of paper was wedged into the bend of the cookie rather than placed inside the hollow portion. This kind of cookie is called tsujiura senbei (辻占煎餅) and is still sold in some regions of Japan, especially in Kanazawa, Ishikawa.It is also sold in the neighborhood of Fushimi Inari-taisha shrine in Kyoto.

Makoto Hagiwara of Golden Gate Park's Japanese Tea Garden in San Francisco is reported to have been the first person in the U.S. to have served the modern version of the cookie when he did so at the tea garden in the 1890s or early 1900s. The fortune cookies were made by a San Francisco bakery, Benkyodo.