According to the body, Mr Boucher is leaving to pursue work within the not-for-profit sector and to concentrate on studying.
In the post he was responsible for overseeing the SECâs information technology system including the implementation of security and infrastructure enterprises.
Mr Boucher headed up the Office of Information Technology, which was set up to include IT with all of the SECâs programs of regulation.
Mary L Schapiro, chairman of the SEC, said: âEffective securities regulation depends in large part on making sense of the immense volume of data generated in our securities markets.
âCharlie has played an important role in building a platform to implement our new system for reviewing complaints, tips and investigative leads provided by whistleblowers or other sources.â
The departing CIO added that he saw his time with the SEC as âamong the most important and rewarding of [his] careerâ.
Previously, Mr Boucher worked for Standard & Poorâs as CIO and as an executive director at Morgan Stanley.
By Jim Ottewill