The mosque was built in 1546 and is located within the burial complex of Ki Ageng Henis. This cemetery area was once his residence. Upon his death, he was buried at the site of his former home.

Ki Ageng Henis and Sultan Hadiwijaya were both relatives and close companions. Ki Ageng Henis was the son of Ki Ageng Selo, while Sultan Hadiwijaya was the son of Ki Kebo Kenongo, also known as Ki Ageng Pengging. Ki Ageng Selo and Ki Kebo Kenongo were closely related and both descended from the Majapahit lineage.

Before becoming a kingdom, Pajang was a regency under the rule of the Demak Sultanate. At that time, Hadiwijaya—then known as Joko Tingkir—became the son-in-law of Sultan Trenggono, the ruler of Demak. Joko Tingkir later ascended the throne with the title Sultan Hadiwijaya, while Ki Ageng Henis was appointed as his chief minister (patih) in Pajang.

In front of the mosque flows the Jenes River, which once served as a vital economic artery of the Pajang Kingdom. The river, which joins with the Bengawan Solo, was an important route for trade and transportation.

The Ki Ageng Henis Mosque played a significant role in the founding of the Pajang Kingdom, which later evolved into the Mataram Dynasty. Changes in the mosque’s management over time also influenced its architectural form. Pakubuwana X introduced elements of palace architecture into Masjid Laweyan, which is reflected in the design of the wooden pillars (soko) and roof supports (meret), crafted from teakwood in a style similar to that of the Surakarta Palace.