(CNN) -- Alan D. Bersin, commissioner of the 57,000-employee U.S. Customs and Border Protection, will resign effective December 30, he said Thursday.
Bersin was appointed to the post by President Barack Obama on March 27, 2010. He notified the president of his resignation Thursday, he said in a statement.
Deputy Commissioner David V. Aguilar will serve as acting commissioner, the U.S. Department of Homeland Security said Thursday.
"My service as commissioner has been one of the most rewarding experiences of my public life," Bersin said. "I am immensely proud of the significant and meaningful achievements we have made on our borders and at our nation's ports of entry over nearly two years.
"Through innovative solutions and strengthened partnerships, we have measurably strengthened border security, enhanced our ability to prevent potential terror threats, streamlined the entry process for lawful trade, and expanded our trusted traveler programs," he added.
Homeland Security Secretary Janet Napolitano commended Bersin's service.
"During his tenure, CBP has taken historic steps to secure our borders while facilitating legal travel and trade," Napolitano said in a written statement. "Commissioner Bersin has also been instrumental in facilitating new international agreements and public-private partnerships as well as developing new paradigms throughout the world in combating terrorism and international crime."
In prior positions, Bersin served as California's secretary of education between July 2005 and December 2006 under Republican Gov. Arnold Schwarzenegger's administration and was one of Schwarzenegger's appointees to the State Board of Education, where he served until 2009.
He was also superintendent of San Diego's schools between 1998 and 2005.
Before leading the nation's eighth largest urban school district, he was appointed by President Bill Clinton, a Democrat, as the U.S. attorney for the Southern District of California, a post he held for almost five years.