The former Concord Rangers and Stevenage striker has re-signed for the National League South outfit after a spell at Cressing Road last season before the campaign was cancelled.
Maldon & Tiptree boss Brown replaced Steve Ball at the helm in February, with the U’s alarming loss of form resulting in fears the club could drop into Non-League football.
The former Aveley, Maldon & Tiptree, Thamesmead and Stanway Rovers boss has been with the club since last June but will now take the top job alongside former Leyton Orient, Brentford, Reading and Sutton player John Mackie.
Brown, a former Colchester captain, assistant and caretaker manager, was given the nod to take over at Colchester after breaking records at Essex neighbours Maldon & Tiptree.
With Non-League Steps 3 to 6 curtailed for the second successive season, Brown has been able to take the reins at the League Two strugglers on an interim basis