Culpeper had close access and often came into contact with the Queen and her attendants. Thomas Culpeper was first introduced into Catherine Howard’s personal life in March 1541, when King Henry VIII went on a trip to Dover and left Catherine behind at Greenwich. At this time Culpeper began asking favours of Catherine, who was his seventh cousin, once removed. The private meetings between them are thought to have begun sometime around May of that same year. Catherine’s lady-in-waiting the Lady Rochford, arranged the meetings between Culpeper and Catherine. On these occasions only she and another lady-in-waiting, Katherine Tilney, were allowed entrance to the Queen’s chamber.
On June 30, Catherine and King Henry VIII travelled north to York in the hope of meeting James V of Scotland. They arrived at Lincoln on August 9, where Culpeper met Catherine for another secret meeting in her bedchamber. These meetings continued in Pontefract Castle, after the court arrived on August 23. It is believed that the infamous letter Catherine sent to Culpeper was sent during these proceedings. In this letter she wishes to know how he is and is troubled that he is ill. Catherine also writes, “I never longed so muche for [a] thynge as I do to se you and to speke wyth you, the wyche I trust shal be shortely now,” and “my trust ys allway in you that you wolbe as you have promysed me...” These statements cause some audiences to believe that their affair was not one of passion, but rather centred towards Culpeper’s political agenda. With Henry in poor health and only his very young son Edward to succeed him, being Catherine's favourite would undoubtedly have put Culpeper in a very strong political position. As a well-liked member of the King’s Privy Chamber he enjoyed a close relationship with Henry. If the promise Catherine mentioned was in reference to his possible knowledge about her previous sexual relationships, Culpeper was most likely using this as leverage to gain power and control over the Queen herself. In her letter Catherine states that she longs to talk with Culpeper but does not mention any desire to be intimate with him.
Stories of the Queen's premarital indiscretions had meanwhile come to the attention of Thomas Cranmer, then Archbishop of Canterbury. During Cranmer's investigations, he came across rumours of an affair between the Queen and Culpeper; Culpeper was soon arrested for questioning. Both he and the Queen denied the allegations, but the letter from Catherine to Culpeper, found during a search of Culpeper's quarters, provided the evidence for which Cranmer was looking. Whether the association between Culpeper and the Queen was ever consummated is still debated by historians, but the letter seems to give evidence of Catherine's feelings for Culpeper. Also in the letter was a reference to Jane Boleyn, Lady Rochford.