James may have had some affection for his mother, though exactly how much is hard to gauge from the source material. James was separated from his mother early in his life, and often there was open hostilities in Scotland between factions supporting James against his Catholic mother. James was crowned King of Scotland at 13 months old, and Mary had been forced to sign documents abdicating the throne to her son (Croft, King James, pp. 11-12). James was raised independently of his mother in order to assure his adherence to a Protestant faith, and to ensure that his mother was not able to either reclaim the throne or unduly influence her son. Over the course of the 20 years following James' birth, Mary made several attempts to reclaim the throne, whether through French support, or in attempts to seize her infant/adolescent son. The open hostility between Marian Catholics and Jacobean Protestants likely colored James' view of his mother.

During the lead up to the execution of Mary, James wrote several letters to John Dudley (Earl of Leicester) and Queen Elizabeth begging them to spare his mother's life. James wrote to Elizabeth that he understood that it was members of Parliament and her advisers that pressed for the execution of Mary, claiming that Elizabeth was in danger so long as Mary lived. Whether this was in the spirit of criticizing bad counselors instead of attacking the monarch directly, is not clear from the text. Akrigg finds James' sympathy for Elizabeth genuine (Akrigg, Letters of King James VI & I, p. 79). James did break off diplomatic ties with England for a brief period following Mary's execution. However, they were reopened by the time of the Spanish Armada, about 16 months later (Croft, p. 22; Akrigg, pp. 87-88). James was upset with Elizabeth for her involvement and her ultimate consent to the proceedings of the execution. Though again, this seems to come from a place of politics and theology, as he argues in his letter to Elizabeth about how Elizabeth should not establish precedent of one monarch killing another (Akrigg, pp. 81-83). From the available material, Elizabeth was pressured into executing her cousin. One of her most important advisers and administrators, Francis Walsingham, was a strong advocate for Mary's death, and the difference of opinion between Walsingham and Elizabeth put a strain on their professional relationship (Guy, Elizabeth: The Forgotten Years, pp. 29-30, 84-85). James may have blamed William Cecil (Lord Burghley) or Walsingham, but James never had to have extended working relationships with them. James did not hold any ill will towards Burghley's son, Robert Cecil, in the numerous letters the two exchanged in the decade before his ascension to the English crown (EG, Bruce, ed. Correspondence of King James VI of Scotland with Sir Robert Cecil).

Akrigg claims that James bore his mother no "filial affection-it would be absurd for him to pretend such feeling for a woman he could not remember ever having seen. His motives were political...and her execution would be flagrant violation of the Law of Divine Right, so dear to James..." (pp. 78-80). James himself wrote that Scotland could not be at peace so long as his mother was alive (Croft, p. 22). While perhaps Akrigg goes too far in his analysis, it is worth noting that James rarely if ever protested the imprisonment or exile of his mother. Mary's numerous planned plots and coups against Elizabeth made her a real danger to the stability of Anglo-Scottish relations, which James spent most of the 1580s trying to buttress. From the sources available, James may have had some attachment to his mother, but it was not a strong bond by any means. After her death and his coronation in England, he had Mary's remains re-interred at Westminster Abbey with a proper tomb for a monarch. Perhaps this was a son's duty to his mother, but more likely it was a monarchs obligation to one of their own.