Yes, you can use Yarn with Deno's JavaScript Registry (JSR). The documentation states that JSR packages can be seamlessly consumed by any tool that uses folders, which includes Yarn. You can incrementally adopt JSR packages in your Node projects, and you can use your favorite npm-compatible package manager like Yarn, or pnpm with JSR.
Keep in mind that while you can use Yarn with JSR, Deno itself has its own module resolution system that does not rely on or package managers like Yarn. Deno's cache system is designed to work with its own module resolution, which fetches and caches modules based on URLs.