diff -u b/core/includes/install.core.inc b/core/includes/install.core.inc
--- b/core/includes/install.core.inc
+++ b/core/includes/install.core.inc
@@ -302,8 +302,9 @@
   // Allow command line scripts to override server variables used by Drupal.
   require_once __DIR__ . '/bootstrap.inc';
 
-  // Prime the drupal_get_filename() cache with the location of the system
-  // module.
+  // Before having installed the system module and being able to do a module
+  // rebuild, prime the drupal_get_filename() static cache with the module's
+  // exact location.
   drupal_get_filename('module', 'system', 'core/modules/system/system.info.yml');
 
   // If the hash salt leaks, it becomes possible to forge a valid testing user
@@ -1033,9 +1034,11 @@
   // system.module in order to work.
   file_ensure_htaccess();
 
+  // Before installing the user module, perform a module rebuild so we know
+  // where the user module is located.
+  system_rebuild_module_data();
   // Enable the user module so that sessions can be recorded during the
   // upcoming bootstrap step.
-  system_rebuild_module_data();
   \Drupal::service('module_installer')->install(array('user'), FALSE);
 
   // Save the list of other modules to install for the upcoming tasks.
diff -u b/core/includes/install.inc b/core/includes/install.inc
--- b/core/includes/install.inc
+++ b/core/includes/install.inc
@@ -923,6 +923,8 @@
   // Collect requirement testing results.
   $requirements = array();
 
+  // Performs an ExtensionDiscovery scan as the system module is unavailable and
+  // we don't yet know where all the modules are located.
   $listing = new ExtensionDiscovery(\Drupal::root());
   $module_list = $listing->scan('module');
   foreach ($info['dependencies'] as $module) {
diff -u b/core/lib/Drupal/Core/Config/InstallStorage.php b/core/lib/Drupal/Core/Config/InstallStorage.php
--- b/core/lib/Drupal/Core/Config/InstallStorage.php
+++ b/core/lib/Drupal/Core/Config/InstallStorage.php
@@ -159,6 +159,8 @@
     if (!isset($this->folders)) {
       $this->folders = array();
       $this->folders += $this->getCoreNames();
+      // Perform an ExtensionDiscovery scan as we cannot use drupal_get_path()
+      // yet because the system module may not yet be enabled during install.
       $listing = new ExtensionDiscovery(\Drupal::root());
       if ($profile = drupal_get_profile()) {
         $profile_list = $listing->scan('profile');
diff -u b/core/lib/Drupal/Core/Extension/ThemeHandler.php b/core/lib/Drupal/Core/Extension/ThemeHandler.php
--- b/core/lib/Drupal/Core/Extension/ThemeHandler.php
+++ b/core/lib/Drupal/Core/Extension/ThemeHandler.php
@@ -512,7 +512,8 @@
     $themes = $this->moduleHandler->buildModuleDependencies($themes);
 
     // Store filenames to allow system_list() and drupal_get_filename() to
-    // retrieve them without having to scan the filesystem.
+    // retrieve them for themes and theme engines without having to scan the
+    // filesystem.
     $this->state->set('system.theme.files', $files_theme);
     $this->state->set('system.theme_engine.files', $files_theme_engine);
 
diff -u b/core/modules/config/src/Tests/ConfigDependencyTest.php b/core/modules/config/src/Tests/ConfigDependencyTest.php
--- b/core/modules/config/src/Tests/ConfigDependencyTest.php
+++ b/core/modules/config/src/Tests/ConfigDependencyTest.php
@@ -184,9 +184,11 @@
       )
     );
     $entity2->save();
+    // Perform a module rebuild so we can know where the node module is located.
+    // and uninstall it.
+    system_rebuild_module_data();
     // Test that doing a config uninstall of the node module deletes entity2
     // since it is dependent on entity1 which is dependent on the node module.
-    system_rebuild_module_data();
     $config_manager->uninstall('module', 'node');
     $this->assertFalse($storage->load('entity1'), 'Entity 1 deleted');
     $this->assertFalse($storage->load('entity2'), 'Entity 2 deleted');
diff -u b/core/modules/simpletest/src/KernelTestBase.php b/core/modules/simpletest/src/KernelTestBase.php
--- b/core/modules/simpletest/src/KernelTestBase.php
+++ b/core/modules/simpletest/src/KernelTestBase.php
@@ -484,6 +484,9 @@
    *   The new modules are only added to the active module list and loaded.
    */
   protected function enableModules(array $modules) {
+    // Perform an ExtensionDiscovery scan as this function may receive a
+    // profile that is not the current profile, and we don't yet have a cached
+    // way to receive inactive profile information.
     $listing = new ExtensionDiscovery(\Drupal::root());
     $module_list = $listing->scan('module');
     // In ModuleHandlerTest we pass in a profile as if it were a module.
diff -u b/core/modules/system/src/Tests/Extension/ModuleHandlerTest.php b/core/modules/system/src/Tests/Extension/ModuleHandlerTest.php
--- b/core/modules/system/src/Tests/Extension/ModuleHandlerTest.php
+++ b/core/modules/system/src/Tests/Extension/ModuleHandlerTest.php
@@ -44,8 +44,11 @@
    * The basic functionality of retrieving enabled modules.
    */
   function testModuleList() {
-    // Build a list of modules, sorted alphabetically.
+    // Prime the drupal_get_filename() static cache with the location of the
+    // testing profile as it is not the currently active profile and we don't
+    // yet have any cached way to retrieve its location.
     drupal_get_filename('profile', 'testing', 'core/profiles/testing/testing.info.yml');
+    // Build a list of modules, sorted alphabetically.
     $profile_info = install_profile_info('testing', 'en');
     $module_list = $profile_info['dependencies'];
 
@@ -192,6 +195,9 @@
     $profile = 'minimal';
     $dependency = 'dblog';
     $this->settingsSet('install_profile', $profile);
+    // Prime the drupal_get_filename() static cache with the location of the
+    // minimal profile as it is not the currently active profile and we don't
+    // yet have any cached way to retrieve its location.
     drupal_get_filename('profile', 'minimal', 'core/profiles/' . $profile . '/' . $profile . '.info.yml');
     $this->enableModules(array('module_test', $profile));
 
diff -u b/core/modules/system/src/Tests/File/ScanDirectoryTest.php b/core/modules/system/src/Tests/File/ScanDirectoryTest.php
--- b/core/modules/system/src/Tests/File/ScanDirectoryTest.php
+++ b/core/modules/system/src/Tests/File/ScanDirectoryTest.php
@@ -28,6 +28,9 @@
 
   protected function setUp() {
     parent::setUp();
+    // Hardcode the location of the simpletest files as it is already known
+    // and shouldn't change, and we don't yet have a way to retreive their
+    // location from drupal_get_filename() in a cached way.
     $this->path = 'core/modules/simpletest/files';
   }
 
diff -u b/core/modules/system/src/Tests/Path/UrlAliasFixtures.php b/core/modules/system/src/Tests/Path/UrlAliasFixtures.php
--- b/core/modules/system/src/Tests/Path/UrlAliasFixtures.php
+++ b/core/modules/system/src/Tests/Path/UrlAliasFixtures.php
@@ -81,7 +81,7 @@
     $tables = array();
 
     // Prime the drupal_get_filename() cache with the location of the system
-    // module.
+    // module as its location is known and shouldn't change.
     drupal_get_filename('module', 'system', 'core/modules/system/system.info.yml');
     module_load_install('system');
     $schema = system_schema();
diff -u b/core/modules/system/system.module b/core/modules/system/system.module
--- b/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -884,11 +884,15 @@
 function _system_rebuild_module_data() {
   $listing = new ExtensionDiscovery(\Drupal::root());
 
-  // Find installation profiles.
+  // Find installation profiles. This needs to happen before
+  // performing a module scan as the module scan requires knowing
+  // what the active profile is.
   $profiles = $listing->scan('profile');
   $profile = drupal_get_profile();
   if ($profile && isset($profiles[$profile])) {
-    // Prime drupal_get_filename() with the profile info file location.
+    // Prime the drupal_get_filename() static cache with the profile info file
+    // location so we can use drupal_get_path() on the active profile during
+    // the module scan.
     drupal_get_filename('profile', $profile, $profiles[$profile]->getPathname());
   }