The visitors opened the match well as they dominated possession and pounded the Blackpool goalmouth as the Seasiders were put under pressure for long spells.
Blackpool's best chance of the half came after 40 minutes when Adrian Forbes mis-kicked from just six yards out as he wasted a golden opportunity to break the deadlock.
Town quickly broke forward catching Blackpool unawares. Jason Crowe beat Robbie Williams on the wing before whipping in a good ball across goal that split the Blackpool defence, Simon Cox coolly grabbing the opener.
After the break Brandon replaced out-of-form Forbes and the Seasiders looked a different side. Brandon made his mark just four minutes after coming on as he found a way through the Cobblers defence before blasting home an equaliser.
The newly invigorated Seasiders lifted the pace and, just three minutes later, Wes Hoolahan's corner was handled in the box by Sean Dyche before the young winger stepped up himself to convert the spot kick.
The visitors almost hit back with Brett Johnson finding a hole down the left and his ball across from the touchline came agonisingly close to being converted.
Johnson injured himself in the process and Blackpool were quick to react to a now ten-man opposition.
After 62 minutes Keigan Parker again picked out Brandon who found himself in acres of space just eight yards out as he slotted home Blackpool's third.
The misery continued for the now subdued visitors as Blackpool refused to allow them back into the match.
Hoolahan again worked the defence on the break before his cross was turned in by the somewhat unfortunate Dyche to hammer the final nail into Northampton's coffin.