You are looking for a GP tool [`Create SQLite Database`][1] available since 10.4 (previously, in 10.3, you had to use an `arcpy` function [`CreateSQLiteDatabase()`][2].

Choose as `spatial_type` parameter `GEOPACKAGE` which will create an [OGC GeoPackage dataset][3]. This is essentially an SQLite database with ST_Geometry storage plus some extra OGC features.

You can use this workspace very much like any SQLite geodatabase, that is load/export feature classes and tables and create views. You can read more about support for SQLite in ArcGIS in this help topic [SQLite and ArcGIS][4].
 


  [1]: http://desktop.arcgis.com/en/arcmap/10.4/tools/data-management-toolbox/create-sqlite-database.htm
  [2]: http://desktop.arcgis.com/en/arcmap/10.3/analyze/arcpy-functions/createsqlitedb.htm
  [3]: http://www.opengeospatial.org/standards/geopackage
  [4]: http://desktop.arcgis.com/en/arcmap/10.3/manage-data/databases/sqlite-and-arcgis.htm