The Blades have suffered a dip in form and last night lost 2-0 to Crawley at Bramall Lane.
Despite that, their chances of promotion remain alive. Chris Morgan, the first-team coach, has been placed in temporary charge.
Wilson departed after talks with the club on Wednesday evening, and his assistant Frank Barlow follows him out.
"We must thank Danny and Frank for all their endeavours and hard work over the past two seasons," said Sheffield United owner Kevin McCabe.
"We now have a mini season for this club to achieve success and we will all back Chris in this mission."