Carlisle, who played under Boothroyd at Watford, spent the second half of the season on loan at Sixfields from Burnley and was an ever-present in the Town team since his arrival at the League Two club on deadline day in January.
The 32-year-old was an integral cog as Northampton staved off the threat of relegation from the Football League but Boothroyd is aware he faces some stiff competition for the experienced defender's signature.
"Conversations with Clarke are ongoing," said Boothroyd following the final game of the season at Rotherham on Saturday. "He will have a lot of offers and we have got to put an offer together for him and make sure all the little things that are important in his life are right for him."
Boothroyd also plans to begin contract negotiations with goalkeeper Neal Kitson and defender Anthony Charles this week.
"Neal had a brilliant start, he was saving penalties and it was real Roy of the Rovers stuff," added the Town boss. "Anthony has impressed me as a person and you have got to get the character right before anything else and both players are at it so I will speak to both of them this week and decide where we go from here with it."
