Rabbi Dov Zakheim's refused to tell journalists the exact reason for his departure on Wednesday.
However, he hinted that the task of controlling hundreds of billions of dollars in the Bush administration was exhausting.
"I'm leaving because I've served three very arduous years in this job."
A former adjunct economics professor at New York's Yeshiva University, Rabbi Zakheim has spent more than 30 years working in various jobs at the Pentagon.
But he has also worked in private industry, specifically as a consultant to McDonnell Douglas and Boeing.
A conservative Republican who graduated from Jew's College in London in 1973, Zakheim first joined the Department of Defence in 1981 under former president Ronald Reagan.
"I'm leaving because I've served three very arduous years in this job"
Rabbi Dov Zakheim,
Pentagon comptroller and chief financial officer
He was responsible for such tasks as preparing defence planning guidance for nuclear war.
Stressful Bush years
The rabbi was a senior foreign policy adviser to then - Governor George Bush during the 2000 presidential campaign.
As Pentagon Comptroller and Chief Financial Officer, Rabbi Zakheim's priority has been financial management.
He had intended to focus his energies on bringing business practices to the bureaucratic business of defence procurement.
But due to the wars in Afghanistan and Iraq, he was forced to prepare numerous supplemental budget requests for Congress to cover the cost of those military conflicts.
The Pentagon has asked Congress for a record $401.7 billion budget for 2005.
But that does not include additional spending needed to support US wars in Iraq and Afghanistan - a sum expected to range from $30 billion to $50 billion.
Though the US Defence Department has long been notorious for waste, recent government reports suggest the Pentagon's money management woes have reached astronomical proportions.
A study by the Defense Department's inspector general found that the Pentagon couldn't properly account for more than a trillion dollars in monies spent.
A General Accounting Office report found Defence inventory systems so lax that the US army lost track of 56 aeroplanes, 32 tanks and 36 Javelin missile command launch-units.