The LindowsOS Membership Edition licence also includes one-year access to what the company calls it's "Click-N-Run Warehouse" of software programs which can be downloaded from the company's site.
Educators participating in the flat-rate programme will be able to download educational software as well as receiving the LindowsOS licence.
Many schools get computers donated to them, but they cannot afford to equip them with modern operating systems and software, said Lindows.com chief executive officer Michael Robertson said in a statement.
He added that under the new flat-free programme schools, no matter what their size, would be able to provide their computers with an up-to-date OS.
Lindows.com has made a splash with its low-cost Linux-based OS recently, with widening distribution deals and its showdown with Microsoft.
But despite its legal problems, Lindows has managed to rack up deals with retailers such as Walmart.com, which sells low-cost PCs loaded with the LindowsOS.