Having retired in 2004, Padalino started as assistant coach to cousin[citation needed]Gian Piero Ventura at Hellas Verona, leaving at the end of the season to rejoin the first team at Foggia, as its administrative secretary.
In 2007–08, Padalino rejoined Ventura as his assistant at Pisa, also in the second level.
In 2009–10, Padalino started his career as head coach at Nocerina in the Seconda Divisione until the end of the season.
On 7 August 2012, he was named the new coach of [[A.C.D]. Foggia Calcio|Foggia]] in the Serie D. He led the team to promotion to Lega Pro in 2014 and then left the club.
In November 2014, he became the new manager of Grosseto in the Lega Pro, but he was fired in January 2015, before the end of the season.
On 5 October 2015, he was appointed as the new coach of Matera, ending the season in sixth place in the Lega Pro.
On 13 June 2016, he was named as the new coach of Lecce in the Lega Pro. He was sacked on 24 April 2017 with two games to spare.
He returned into management on 18 December 2018 after being appointed head coach of Foggia, in the Serie B league.[2]
On 13 August 2020, he was hired by Juve Stabia, freshly relegated into Serie C.[3] He left the club at the end of the 2020–21 season.
On 29 December 2021, Padalino was appointed as the new head coach of Serie C club Siena.[4] On 12 May 2022, Siena announced Padalino's departure from the club.[5]
On 30 August 2022, he was signed by Turris, another Serie C club.[6] On 25 October 2022, less than months since his appointment, Padalino tended his resignations and left Turris.[7]
In July 2024, Padalino was hired by Serie C club Latina; he was sacked on 20 October 2024 following a string of negative results.[8]