diff --git a/NEWS.md b/NEWS.md
index e5087ea93..77642d3b5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # pkgdown (development version)
 
+* `build_home()` now supports a `.pkgdownignore` file to exclude markdown files
+  from being rendered to HTML. The file can be placed in the package root,
+  `pkgdown/`, or `_pkgdown/` directories (@kyleGrealis, #2959).
+
 # pkgdown 2.2.0
 
 * Make `build_llm_docs()` more robust to the use of old Pandoc (@nanxstats, @galachad, #2952, #2954)
diff --git a/R/build-home-md.R b/R/build-home-md.R
index ae156b838..507039589 100644
--- a/R/build-home-md.R
+++ b/R/build-home-md.R
@@ -16,6 +16,14 @@ package_mds <- function(path, in_dev = FALSE) {
 
   # Remove files handled elsewhere
   handled <- c("README.md", "LICENSE.md", "LICENCE.md", "NEWS.md")
+
+  # Append user-defined ignores from .pkgdownignore
+  user_ignores <- read_pkgdownignore(path)
+  if (length(user_ignores) > 0) {
+    cli::cli_inform("Ignoring: {user_ignores}")
+  }
+  handled <- c(handled, user_ignores)
+  # handled <- c(handled)
   mds <- mds[!path_file(mds) %in% handled]
 
   # Do not build 404 page if in-dev
@@ -59,3 +67,35 @@ render_md <- function(pkg, filename) {
 
   invisible()
 }
+
+#' Read .pkgdownignore file
+#'
+#' Searches for .pkgdownignore in standard pkgdown config locations.
+#' Returns filenames to exclude (one per line, with comments ignored).
+#'
+#' @param path Path to the package root
+#' @return Character vector of filenames to exclude
+#' @noRd
+read_pkgdownignore <- function(path) {
+  # Check standard pkgdown config locations:
+  candidates <- c(
+    path(path, ".pkgdownignore"),
+    path(path, "_pkgdown", ".pkgdownignore"),
+    path(path, "pkgdown", ".pkgdownignore")
+  )
+
+  # Read output from all ignore files
+  ignore_paths <- candidates[file_exists(candidates)]
+  if (length(ignore_paths) == 0) {
+    return(character())
+  }
+
+  # Combine lines from all ignore files
+  lines <- unlist(lapply(ignore_paths, readLines))
+
+  # Remove comments & empty lines and trim whitespace
+  lines <- lines[!grepl("^\\s*#", lines)]
+  lines <- lines[nzchar(trimws(lines))]
+
+  unique(trimws(lines))
+}
diff --git a/tests/testthat/test-pkgdownignore.R b/tests/testthat/test-pkgdownignore.R
new file mode 100644
index 000000000..3a7b14a4b
--- /dev/null
+++ b/tests/testthat/test-pkgdownignore.R
@@ -0,0 +1,162 @@
+test_that("read_pkgdownignore returns empty when no file exists", {
+  pkg <- local_pkgdown_site()
+  expect_equal(read_pkgdownignore(pkg$src_path), character())
+})
+
+test_that("read_pkgdownignore reads from package root", {
+  pkg <- local_pkgdown_site()
+  write_lines(c("CLAUDE.md", "AGENTS.md"), path(pkg$src_path, ".pkgdownignore"))
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, c("CLAUDE.md", "AGENTS.md"))
+})
+
+test_that("read_pkgdownignore reads from pkgdown/ directory", {
+  pkg <- local_pkgdown_site()
+  dir_create(path(pkg$src_path, "pkgdown"))
+  write_lines("INTERNAL.md", path(pkg$src_path, "pkgdown", ".pkgdownignore"))
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, "INTERNAL.md")
+})
+
+test_that("read_pkgdownignore reads from _pkgdown/ directory", {
+  pkg <- local_pkgdown_site()
+  dir_create(path(pkg$src_path, "_pkgdown"))
+  write_lines("NOTES.md", path(pkg$src_path, "_pkgdown", ".pkgdownignore"))
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, "NOTES.md")
+})
+
+test_that("read_pkgdownignore combines files from multiple locations", {
+  pkg <- local_pkgdown_site()
+
+  # Root
+
+  write_lines("CLAUDE.md", path(pkg$src_path, ".pkgdownignore"))
+
+  # pkgdown/
+  dir_create(path(pkg$src_path, "pkgdown"))
+  write_lines("AGENTS.md", path(pkg$src_path, "pkgdown", ".pkgdownignore"))
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_setequal(result, c("CLAUDE.md", "AGENTS.md"))
+})
+
+test_that("read_pkgdownignore ignores comments and empty lines", {
+  pkg <- local_pkgdown_site()
+  write_lines(
+    c(
+      "# This is a comment",
+      "CLAUDE.md",
+      "",
+      "  # Indented comment",
+      "AGENTS.md",
+      "   ",
+      "INTERNAL.md"
+    ),
+    path(pkg$src_path, ".pkgdownignore")
+  )
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, c("CLAUDE.md", "AGENTS.md", "INTERNAL.md"))
+})
+
+test_that("read_pkgdownignore trims whitespace", {
+  pkg <- local_pkgdown_site()
+  write_lines(
+    c("  CLAUDE.md  ", "\tAGENTS.md\t"),
+    path(pkg$src_path, ".pkgdownignore")
+  )
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, c("CLAUDE.md", "AGENTS.md"))
+})
+
+test_that("read_pkgdownignore deduplicates entries", {
+  pkg <- local_pkgdown_site()
+
+  # Same file in root and pkgdown/
+
+  write_lines("CLAUDE.md", path(pkg$src_path, ".pkgdownignore"))
+  dir_create(path(pkg$src_path, "pkgdown"))
+  write_lines("CLAUDE.md", path(pkg$src_path, "pkgdown", ".pkgdownignore"))
+
+  result <- read_pkgdownignore(pkg$src_path)
+  expect_equal(result, "CLAUDE.md")
+})
+
+test_that("package_mds excludes files listed in .pkgdownignore", {
+  pkg <- local_pkgdown_site()
+
+  # Create test markdown files
+  write_lines("# CLAUDE", path(pkg$src_path, "CLAUDE.md"))
+  write_lines("# AGENTS", path(pkg$src_path, "AGENTS.md"))
+  write_lines("# ROADMAP", path(pkg$src_path, "ROADMAP.md"))
+
+  # Create .pkgdownignore
+
+  write_lines(c("CLAUDE.md", "AGENTS.md"), path(pkg$src_path, ".pkgdownignore"))
+
+  result <- package_mds(pkg$src_path)
+  result_files <- path_file(result)
+
+  expect_false("CLAUDE.md" %in% result_files)
+  expect_false("AGENTS.md" %in% result_files)
+  expect_true("ROADMAP.md" %in% result_files)
+})
+
+test_that("package_mds excludes .github files listed in .pkgdownignore", {
+  pkg <- local_pkgdown_site()
+
+  # Create .github directory with markdown files
+  dir_create(path(pkg$src_path, ".github"))
+  write_lines("# Internal", path(pkg$src_path, ".github", "INTERNAL.md"))
+  write_lines(
+    "# Contributing",
+    path(pkg$src_path, ".github", "CONTRIBUTING.md")
+  )
+
+  # Ignore the internal one
+  write_lines("INTERNAL.md", path(pkg$src_path, ".pkgdownignore"))
+
+  result <- package_mds(pkg$src_path)
+  result_files <- path_file(result)
+
+  expect_false("INTERNAL.md" %in% result_files)
+  expect_true("CONTRIBUTING.md" %in% result_files)
+})
+
+test_that("package_mds works when .pkgdownignore is empty", {
+  pkg <- local_pkgdown_site()
+
+  # Create test file
+  write_lines("# ROADMAP", path(pkg$src_path, "ROADMAP.md"))
+
+  # Empty ignore file
+  file_create(path(pkg$src_path, ".pkgdownignore"))
+
+  result <- package_mds(pkg$src_path)
+  result_files <- path_file(result)
+
+  expect_true("ROADMAP.md" %in% result_files)
+})
+
+test_that("package_mds works when .pkgdownignore has only comments", {
+  pkg <- local_pkgdown_site()
+
+  # Create test file
+  write_lines("# ROADMAP", path(pkg$src_path, "ROADMAP.md"))
+
+  # Ignore file with only comments
+  write_lines(
+    c("# comment 1", "# comment 2"),
+    path(pkg$src_path, ".pkgdownignore")
+  )
+
+  result <- package_mds(pkg$src_path)
+  result_files <- path_file(result)
+
+  expect_true("ROADMAP.md" %in% result_files)
+})