The deficit for the year ending June 30 followed a profit of more than £11million in the 2013-14 campaign.
Revenue fell by more than a fifth to £51.1million, a fall attributed to a drop in transfer income and the failure to reach the Champions League.
Celtic still made a £6.8million gain on transfers but that was down from more than £17million in the previous 12 months.
Celtic sold goalkeeper Fraser Forster to Southampton last summer for £10million while bringing Craig Gordon in for free as his replacement.
Their transfer spending - for the likes of Stefan Scepovic, Stuart Armstrong, Gary Mackay-Steven and a series of loan signings - was listed as £9.4million.
Chairman Ian Bankier said: “These results, which show an operating loss of £3.6million compared to a profit of £11.8million last year, reflect two key factors. First, lower contribution from the sale of player registrations, and second, diminished income from competing in the UEFA Europa League competition.
“The lower contribution from the disposal of player registrations was as a result of the board deciding to retain certain registrations to aid and enhance value for the football operations.”
Celtic have since failed to qualify for the Champions League group stages for a second season but have sold Virgil van Dijk to Southampton in a deal worth a potential £13million.
Bankier added: “The board remains committed to ensuring that the medium and long-term future of the club, and the company, is secured.
“Having regard to the environment in which we continue to operate, the board’s belief in a self-sustaining financial model has not wavered. We believe that there is no other sensible way to operate. The model is designed to protect the club from the inherent unpredictability of football.”
Chief executive Peter Lawwell described the season as a “transition” on the park under new manager Ronny Deila and a “challenging” one off the field.
Lawwell added: “Our decision not to transfer certain players registration during the period, together with failure to progress in the UEFA Champions League, have had a significant impact on revenues and profits.
“Our core strategy remains focused on a football operation with a self sustaining financial model and relies upon: the youth academy; player development; player recruitment; management of the player pool; and sports science and performance analysis, to deliver long-term sustainable football success.”
Lawwell continued: “Our objectives this year remain success in all three domestic competitions and in the UEFA Europa League, playing creative and exciting football.
“We will continue to build on the foundations that have been laid and focus on qualification for the group stages of the UEFA Champions League, which is where this great club belongs.”