diff --git a/jedi/api/__init__.py b/jedi/api/__init__.py
index e75690b5..ac1132be 100644
--- a/jedi/api/__init__.py
+++ b/jedi/api/__init__.py
@@ -31,7 +31,7 @@ from jedi.evaluate import representation as er
 from jedi.evaluate import imports
 from jedi.evaluate.param import try_iter_content
 from jedi.evaluate.helpers import get_module_names, evaluate_call_of_leaf
-from jedi.evaluate.sys_path import get_venv_path
+from jedi.evaluate.sys_path import get_venv_path, dotted_path_in_sys_path
 from jedi.evaluate.iterable import unpack_tuple_to_dict
 from jedi.evaluate.filters import TreeNameDefinition
 
@@ -151,7 +151,10 @@ class Script(object):
             self._get_module_node(),
             self.path
         )
-        imports.add_module(self._evaluator, module.name.string_name, module)
+        if self.path is not None:
+            name = dotted_path_in_sys_path(self._evaluator.sys_path, self.path)
+            if name is not None:
+                imports.add_module(self._evaluator, name, module)
         return module
 
     @property
diff --git a/jedi/evaluate/compiled/mixed.py b/jedi/evaluate/compiled/mixed.py
index 905f4da5..0be5007b 100644
--- a/jedi/evaluate/compiled/mixed.py
+++ b/jedi/evaluate/compiled/mixed.py
@@ -209,6 +209,7 @@ def _create(evaluator, obj, parent_context=None, *args):
     else:
         from jedi.evaluate.representation import ModuleContext
         module_context = ModuleContext(evaluator, module_node, path=path)
+        # TODO this __name__ is probably wrong.
         name = compiled_object.get_root_context().py__name__()
         imports.add_module(evaluator, name, module_context)
 
diff --git a/jedi/evaluate/imports.py b/jedi/evaluate/imports.py
index 2201f991..d0aec515 100644
--- a/jedi/evaluate/imports.py
+++ b/jedi/evaluate/imports.py
@@ -523,9 +523,11 @@ def get_modules_containing_name(evaluator, modules, name):
         with open(path, 'rb') as f:
             code = python_bytes_to_unicode(f.read(), errors='replace')
             if name in code:
-                module_name = os.path.basename(path)[:-3]  # Remove `.py`.
                 module = _load_module(evaluator, path, code)
-                add_module(evaluator, module_name, module)
+
+                module_name = sys_path.dotted_path_in_sys_path(evaluator.sys_path, path)
+                if module_name is not None:
+                    add_module(evaluator, module_name, module)
                 return module
 
     # skip non python modules
diff --git a/jedi/evaluate/sys_path.py b/jedi/evaluate/sys_path.py
index 24bd26b6..a4990c3c 100644
--- a/jedi/evaluate/sys_path.py
+++ b/jedi/evaluate/sys_path.py
@@ -1,6 +1,7 @@
 import glob
 import os
 import sys
+import imp
 from jedi.evaluate.site import addsitedir
 
 from jedi._compatibility import exec_function, unicode
@@ -281,3 +282,33 @@ def _get_buildout_script_paths(module_path):
             debug.warning(unicode(e))
             continue
     return extra_module_paths
+
+
+def dotted_path_in_sys_path(sys_path, module_path):
+    """
+    Returns the dotted path inside a sys.path.
+    """
+    # First remove the suffix.
+    for suffix, _, _ in imp.get_suffixes():
+        if module_path.endswith(suffix):
+            module_path = module_path[:-len(suffix)]
+        break
+    else:
+        # There should always be a suffix in a valid Python file on the path.
+        return None
+
+    if module_path.startswith(os.path.sep):
+        # The paths in sys.path most of the times don't end with a slash.
+        module_path = module_path[1:]
+
+    for p in sys_path:
+        if module_path.startswith(p):
+            rest = module_path[len(p):]
+            if rest:
+                split = rest.split(os.path.sep)
+                for string in split:
+                    if not string or '.' in string:
+                        return None
+                return '.'.join(split)
+
+    return None