Prasad, whose party is expected to have an alliance with the Congress for the next Lok Sabha polls, left for Muzaffarnagar early morning.
His visit is being coordinated by Rajya Sabha member Mohammed Adeeb. Adeeb was made the member of the upper house with the support of the Samajwadi Party and the Congress.
Prasad is expected to visit half a dozen relief camps inhabited by members of the Muslim community.
Prasad is considered a popular leader among the community and his party RJD had been in power in Bihar for 15 years largely on the basis of MY (Muslim-Yadav) combination.
Prasad, who had arrested BJP leader L K Advani during the Ram Janambhoomi movement in the 1990s, has been projecting himself to be a true secular and talking about playing a larger role in halting the march of Narendra Modi-led BJP.
Lalu's visit comes a week after Congress vice president Rahul Gandhi made an unannounced visit to to the riot-hit areas of Muzaffarnagar district and relief camps to meet the affected people from both the Muslim and Hindu communities.