Zheng Xiaoyu was accused of accepting some $850,000 in bribes
He was convicted of taking 6.5m yuan ($850,000; £425,400) in bribes and of dereliction of duty at a trial in May.
The bribes were linked to sub-standard medicines, blamed for several deaths.
China has been criticised over a number of recent cases involving tainted goods, and correspondents say Zheng had become a symbol of the crisis.
Zheng had appealed against his sentence, arguing that it was "too severe" and saying he had confessed his crimes and co-operated with police.
But his appeal, heard in mid-June, was rejected shortly afterwards.
Following Zheng's sacking in 2005, the Chinese government announced an urgent review of about 170,000 medical licences that were awarded during his tenure at the agency.
At a news conference in Beijing on Tuesday the State Food and Drug agency said that its supervision of safety was unsatisfactory, and it vowed to improve matters.
A senior official said Zheng Xiaoyu had "brought shame" on the department, adding that anyone abusing their power would be punished.
Chinese officials have already acknowledged that the country could face social unrest and a further tarnished image abroad unless improvements are made.
Dozens of people have died in China because of poor quality or fake food and drugs, sparking widespread international fears about the safety of Chinese exports.
Thirteen babies died of malnutrition in 2005 after being fed powdered milk that had no nutritional value.
US inspectors have blamed exported Chinese pet food ingredients, contaminated with melamine, for the deaths of cats and dogs in North America.
And they recently halted shipments of toothpaste from China to investigate reports that they may be contaminated with toxic chemicals.
The BBC's Daniel Griffiths in Beijing says the government is hoping that this execution will show it is getting to grips with the crisis.
But food and drug safety standards vary widely across this vast country and reform is going to be a major challenge, he says.