The treatment will be used on patients with gastrointestinal stromal tumors (GlST) who were previously treated with tyrosine kinase inhibitors or anti-cancer drugs.
The EMA filing follows the EU approval in August 2013 of regorafenib (Stivarga) to fight against metastatic colorectal cancer.
Member of Bayer HealthCare executive committee and head of global development Kemal Malik said: "The submission of regorafenib to EMA is an exciting advance because it means patients with GIST will have a potential new treatment option to help manage an aggressive disease."
He added that Bayer looks ‘forward to offering patients and physicians a new path forward’.
European Organisation for Research and Treatment of Cancer (EORTC) president Prof Jean-Yves Blay said: "GIST is a disease that only affects a limited number of people, about 15 per million per year.
"Of those who are affected over half develop recurrent metastatic disease, for which there are currently very few treatment options once resistance to first line treatments are observed."
Gastrointestinal Stromal Tumors (GIST) GIST is the most common form of sarcoma that originates from the muscle wall of the gastrointestinal tract.
It can be a life-threatening disease that has the ability to spread to other parts of the body and cannot be surgically removed.
Stivarga is currently approved in the US, Europe and Japan, for use in the treatment of patients with metastatic colorectal cancer (mCRC).
It has also been approved in the US and Japan for treating GIST.
Image: A hematoxylin-eosin stain of a gastrointestinal stromal tumor of the stomach. Photo: file image.