Kejriwal had failed to file his nomination papers on Monday due to a massive raodshow.
On Tuesday, he arrived early at the RO office, accompanied by his family, including parents, and party leaders Pankaj Gupta and Gopal Mohan.
Kejriwal is fighting polls from the New Delhi Assembly seat.
"The journey for the next five years starts from here. Like the good work that has happened in Delhi, I hope in the next five years also there will be good work," he said while talking to the media before filing his nomination papers.
He said: "Parties are forming alliance in Delhi against the AAP, in an unprecedented move."
"The BJP, Congress and many other parties have come together... the LJP, JJP, JD(U) and RJD. For the first time there is such a coalition in Delhi. All these parties only have one aim: 'defeat Kejriwal'.
"And I have only one aim, how to end corruption and take Delhi forward. They are saying 'defeat Kejriwal', I am saying make schools better, hospitals better, give electricity. Their only aim is to defeat Kejriwal," the AAP chief added.
There was a huge crowd of candidates at the SDM office since morning as Tuesday was the last date for filing nomination.
The supporters of other candidates accused the police of giving "VIP treatment" to the Chief Minister. Kejriwal faced protest from the candidates and their supporters contesting against him at the RO office.
( With inputs from IANS )