It was founded by the Society of Jesus, commonly known as the Jesuits, in 1865 as the Observatorio Meteorológico del Ateneo Municipal de Manila.

After initial hesitation on the part of the Jesuits because of the primitive instruments available, the superior yielded upon the promise of a Secchi Universal Meteorograph purchased from the Holy See.

[1] The American colonial government established the observatory in 1901 as the Philippine Weather Bureau, which expanded into meteorology, astronomy, and geomagnetism.

In 1963 it was transferred to the Loyola Heights campus of Ateneo de Manila University where it continues its studies into seismology, geomagnetism, and radio physics, among other areas of research.

Research programs include Climate Change Assistance, Geomatics for Environment and Development, Instrumentation and Technology, Regional Climate Systems, Solid Earth Dynamics, Air Quality Dynamics, and Special Research Projects.