The development of cTAKES started in 2006 by a team of physicians, computer scientists and software engineers at the Mayo Clinic. The development team was led by Dr. Guergana Savova & Dr. Christopher Chute. cTAKES is released open source under an Apache v2.0 license. This system was deployed at Mayo and is currently an integral part of their clinical data management infrastructure and has processed in excess of 80 million clinical notes.

Following Dr. Savova's move to Children's Hospital Boston in early 2010, the core development team expanded to include Mayo Clinic and Children's Hospital Boston. Additional collaborations with external groups at University of Colorado, Brandeis University, University of Pittsburgh, University of California at San Diego continue to extend the capabilities of cTAKES into areas such Temporal Reasoning, Clinical Question and Answering, and coreference resolution for the clinical domain. In 2010, cTAKES was adopted by the I2B2 program and is a central component of the SHARP Area 4.

On June 11, 2012, cTAKES entered the Apache Incubator. On March 20, 2013, cTAKES graduated into an Apache TLP.