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He had been with Scarborough since last summer, he joined them after being released from Glanford Park.
As the two clubs could not agree a suitable fee, a transfer tribunal was convened to rule on the switch.
Northampton must pay an initial £30K to Boro, with the rest coming in three £5K installments.
Scarborough will also receive 10% of any future fee for the forward.
"I am disappointed at the level of fee received for Darryn," explained Scarborough chairman Malcom Reynolds to their official website.
"Whilst we valued Darryn at much higher, we had asked the tribunal to specify a fee in the region of £60,000 to show how keen we were to resolve this issue.
"We are however keen to put this behind us and look forward to replacing Darryn shortly."
According to leading unofficial Boro website Seadogs Online the player Boro are chasing is experience Dover Athletic frontman Keith Scott.