Ms Ackroyd said during the hearing that she felt victimised by the BBC and made a scapegoat following an internal inquiry into the BBC's use of freelancers.
It is believed that at least 100 past and current BBC presenters are being investigated for alleged tax avoidance through personal service companies.
HMRC claimed that she owed a total of £419,151 in outstanding tax and NICs for this period.
Ms Ackroyd was the BBC's highest-paid regional presenter until she was let go in 2013, with a salary of £163,000 plus a performance-related bonus.
This is the first judgment among a number of appeals involving television presenters. Last year's change to the way IR35 works in the public sector has essentially stopped contracting in the sector altogether, robbing it of vital specialist skills and damaging public services.
Ms Ackroyd, who lives near Halifax, broke her silence to describe "five horrendous years of innuendo and gossip" since she was abruptly taken off screen. It ruled that the services she had provided had been delivered under a contract directly between the BBC and Ms Ackroyd, rendering her in effect an employee of the organisation for income tax purposes.
Dave Chaplin, founder of Contractor Calculator, an website for freelancers and contractors added: "I have a lot of sympathy for Christa Ackroyd".
She added that it showed the importance of seeking advice from appropriately qualified professionals who have a good understanding of IR35 issues, and urged "freelancers and contractors to review their IR35 status" immediately, as they may face scrutiny by HMRC. "HMRC is coming, you need to prepare", he said.
A BBC spokesman says: "The BBC was not party to this case, and as was standard industry practice at the time the individual was engaged as a freelancer in 2001 and paid via their existing company. Until past year it was for individuals with service companies, rather than those engaging them, to determine their status for tax purposes".
"The use of personal service companies is entirely legitimate and common practice across the industry as it provides flexibility for both individuals and organisations".
HMRC claimed that as an employee of CAM, the company was liable for income tax and national insurance payments.