The tenure of the chairman is for three years. Until now, Health Secretary Bhanu Pratap Sharma was temporarily in-charge of the post.
"I will assume office this week. It is a new and challenging role," Mr Bahuguna told PTI.
Mr Bahuguna, a 1978-batch Indian Administrative Service officer of Rajasthan cadre, retired in February this year.
The position of chairman of food safety regulatory body was lying vacant since January this year when the tenure of K Chandramouli ended.
The FSSAI has lately been in the news after it banned Nestle's instant noodles Maggi for being "unsafe and hazardous" for human consumption after it found excessive levels of lead and presence of taste enhancer monosodium glutamate (MSG).
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