In the 2006 NFL game against Tyrone, Brogan was sent off for two yellow card offences and suspended for eight weeks in accordance with Rule 140. Brogan, Ciarán Whelan, Bryan Cullen and Kevin Bonner, along with Tyrone's Kevin Hughes, Michael McGee and Owen Mulligan were exonerated of all charges, the official reason given being 'a technicality'.
In 2006, he won his first All Star in the half forward line for his performances with Dublin. Seán Boylan named him in his compromise rules squad to play Australia in the first test at Pearse Stadium on 29 October 2006. Brogan was named on the inaugural GPA Gaelic Team of the Year which began in 2006. He was named at centre half-forward on the 2006 Dublin Bus/Evening Herald Blue Star football XV.