Thank you, Alexis, and good afternoon, everyone. As Alexis mentioned, total revenue in the third quarter was $4.1 million, a 12.2% decline from last year. The decline reflects the slow recovery from COVID exacerbated by the summer's Delta variant as well as unexpected downtime of our PBRT system. Third quarter revenue from the proton therapy system installed at Orlando Health in Florida was $1.3 million, a year-over-year decrease of 23.4%. The lower volumes were offset by higher average reimbursement per fraction.
Total proton therapy fractions declined by a little over 40% to 973. This was primarily due to the continued impact of COVID-19 as treatment volumes continue to lag from pre-pandemic levels, and the downtime required to repair certain of the systems' components.
Gamma Knife revenue decreased 5.9% to $2.8 million. The decline was due to a decrease in procedures offset by an increase in average reimbursement. The increase in average reimbursement resulted from the expiration of a contract in the fourth quarter that was reimbursed at a lower rate as well as an increase in the average rate at the company's retail sites.
Gamma Knife procedures decreased by 10.9% to 336 for the third quarter, primarily due to the expiration of 1 contract in the fourth quarter of 2020 and another contract in the first quarter of 2021, both high-volume customers. On a same-store basis, Gamma Knife revenues -- Gamma Knife volumes for same centers in operation increased 11.6% from the Gamma Knife volumes for those same centers during the same period of the prior year.
Gross margin increased 29% to $1.5 million compared to $1.1 million for the 2020 third quarter. The increase was primarily due to a 32.7% decrease in depreciation and amortization, result of the year-end balance sheet restructuring as well as the 1 contract expiration in second -- fourth quarter 2020 and 1 in first quarter 2021.
Other direct operating costs decreased 26.4%, primarily due to the 1 contract expiration in the first quarter of 2021 and a decrease in operating costs for the company's existing retail sites. The gross margin percentage was 35.8% in the current quarter compared to 24.4% in the third quarter a year ago, and was essentially even with the second quarter 2021 level of 35.9%.
Selling and administrative costs decreased by 1.4% to $1.1 million due to lower legal, accounting and tax fees. Interest expense decreased 36.2% to $162,000 compared to $254,000 for the same period in the prior year. This decrease reflects the benefit from the April refinancing of the majority of our existing debt and finance lease portfolio at a lower effective interest rate than the company's historic portfolio rate.
Operating income for the quarter was $186,000 compared to an operating loss of $251,000 in the third quarter of 2020. This was a positive swing of $437,000 and reflects the lower direct operating costs and interest expense. As Ray mentioned, operating income was positive for the third consecutive quarter. With the restructuring, refinancing and other cost initiatives, we believe that this trend is sustainable.
We recently received 2022 reimbursement rates from the Centers for Medicare and Medicaid. The delivery code reimbursement rate for a Medicare Gamma Knife treatment has been set at approximately $7,943, an increase of 2.2% from the 2021 rate of $7,773. The approximate CMS reimbursement rate for delivery of PBRT for a simple treatment without compensation will be $554 in 2022 compared to $543 in 2021, and $1,321 compared to $1,298 in 2021 for simple with compensation, intermediate and complex treatments, respectively.
In the fourth quarter, we expect to complete a Cobalt-60 reload and software upgrades for a customer who recently extended their contract to 5 years. In the third quarter, we signed another contract extension as well. The upgrade at Gamma Knife Center Ecuador is now expected to be completed in mid-2022. It will be one of the few Gamma Knife units in all of South America. We continue to have many discussions with existing and potential clients for expanded radiation therapy system products.
This concludes the formal part of our presentation. Carrie, we'd like to now turn the call back over to you for questions.