RaQualia was launched from Pfizer Inc.'s Research Laboratories in Japan. This research facility served as one of Pfizer's discovery research bases and conducted drug discovery research primarily in pain and gastrointestinal disease. In January 2007, Pfizer decided to close the facility as part of a global restructuring of its R&D and business operations.

Then-Director Dr. Atsushi Nagahisa (President and CEO of RaQualia) and over 70 staff from the Laboratories decided to form an R&D-oriented drug discovery company from the primary functions of the facility.

The company was founded in February 2008. In July 2008, RaQualia assumed the former Central Laboratories' human resources, physical assets, and R&D portfolio, and began business.

In July 2011, RaQualia listed on the Osaka Securities Exchange's JASDAQ Growth Market.