Is it possible to set startDestination conditionally using Android Navigation Architecture Component(Android Jetpack)?

Finally, I got a solution to my query...

Put below code in onCreate() method of Activity.

Kotlin code

val navHostFragment = (supportFragmentManager.findFragmentById(R.id.home_nav_fragment) as NavHostFragment)
val inflater = navHostFragment.navController.navInflater
val graph = inflater.inflate(R.navigation.nav_main)
graph.setDefaultArguments(intent.extras)
graph.startDestination = R.id.fragment1
//or
//graph.startDestination = R.id.fragment2

navHostFragment.navController.graph = graph

Java code

NavHostFragment navHostFragment = (NavHostFragment) getSupportFragmentManager().findFragmentById(R.id.home_nav_fragment);  // Hostfragment
NavInflater inflater = navHostFragment.getNavController().getNavInflater();
NavGraph graph = inflater.inflate(R.navigation.nav_main);
graph.setDefaultArguments(getIntent().getExtras());
graph.setStartDestination(R.id.fragment1);

navHostFragment.getNavController().setGraph(graph);
navHostFragment.getNavController().getGraph().setDefaultArguments(getIntent().getExtras());


NavigationView navigationView = findViewById(R.id.navigationView);
NavigationUI.setupWithNavController(navigationView, navHostFragment.getNavController());

Additional Info

As @artnest suggested, remove the app:navGraph attribute from the layout. It would look something like this after removal

<?xml version="1.0" encoding="utf-8"?>
<FrameLayout xmlns:android="http://schemas.android.com/apk/res/android"
    xmlns:app="http://schemas.android.com/apk/res-auto"
    xmlns:tools="http://schemas.android.com/tools"
    android:layout_width="match_parent"
    android:layout_height="match_parent">

    <androidx.fragment.app.FragmentContainerView
        android:id="@+id/home_nav_fragment"
        android:name="androidx.navigation.fragment.NavHostFragment"
        android:layout_width="match_parent"
        android:layout_height="match_parent"
        app:defaultNavHost="true" />

</FrameLayout>

In the case of a fragment tag used instead of FragmentContainerView, the above changes remain the same

Some of the APIs have changed, are unavailable or are not necessary since Akash's answer. It's a bit simpler now.

MainActivity.java:

@Override
protected void onCreate(Bundle savedInstanceState) {
  super.onCreate(savedInstanceState);
  setContentView(R.layout.activity_main);

  NavHostFragment navHost = (NavHostFragment) getSupportFragmentManager().findFragmentById(R.id.fragment_main_nav_host);
  NavController navController = navHost.getNavController();

  NavInflater navInflater = navController.getNavInflater();
  NavGraph graph = navInflater.inflate(R.navigation.navigation_main);

  if (false) {
    graph.setStartDestination(R.id.oneFragment);
  } else {
    graph.setStartDestination(R.id.twoFragment);
  }

  navController.setGraph(graph);
}

activity_main.xml:

<?xml version="1.0" encoding="utf-8"?>
<androidx.constraintlayout.widget.ConstraintLayout 
  xmlns:android="http://schemas.android.com/apk/res/android"
  xmlns:app="http://schemas.android.com/apk/res-auto"
  xmlns:tools="http://schemas.android.com/tools"
  android:layout_width="match_parent"
  android:layout_height="match_parent"
  tools:context=".MainActivity">

  <!-- Following line omitted inside <fragment> -->
  <!-- app:navGraph="@navigation/navigation_main" -->
  <fragment
    android:id="@+id/fragment_main_nav_host"
    android:layout_width="match_parent"
    android:layout_height="match_parent"
    android:name="androidx.navigation.fragment.NavHostFragment"
  />

</androidx.constraintlayout.widget.ConstraintLayout>

navigation_main.xml:

<?xml version="1.0" encoding="utf-8"?>
<!-- Following line omitted inside <navigation>-->
<!-- app:startDestination="@id/oneFragment" -->
<navigation xmlns:android="http://schemas.android.com/apk/res/android"
  xmlns:app="http://schemas.android.com/apk/res-auto"
  xmlns:tools="http://schemas.android.com/tools"
  android:id="@+id/navigation_main"
  >

  <fragment
    android:id="@+id/oneFragment"
    android:name="com.apponymous.apponymous.OneFragment"
    android:label="fragment_one"
    tools:layout="@layout/fragment_one"/>
  <fragment
    android:id="@+id/twoFragment"
    android:name="com.apponymous.apponymous.TwoFragment"
    android:label="fragment_two"
    tools:layout="@layout/fragment_two"/>
</navigation>

This can be done with navigation action. Because fragmentA is your start destination, so define an action in fragmentA.

Note these two fields: app:popUpToInclusive="true" app:popUpTo="@id/fragmentA"

<navigation xmlns:android="http://schemas.android.com/apk/res/android"
   xmlns:app="http://schemas.android.com/apk/res-auto"
   xmlns:tools="http://schemas.android.com/tools"
   android:id="@+id/lrf_navigation"
   app:startDestination="@id/fragmentA">

   <fragment
       android:id="@+id/fragmentA"
       android:name="com.mindinventory.FragmentA"
       android:label="fragment_a"
       tools:layout="@layout/fragment_a">

    <action android:id="@+id/action_a_to_b"
            app:destination="@id/fragmentB"
            app:popUpToInclusive="true"
            app:popUpTo="@id/fragmentA"/>
   <fragment>

   <fragment
       android:id="@+id/fragmentB"
       android:name="com.mindinventory.FragmentB"
       android:label="fragment_b"
       tools:layout="@layout/fragment_b"/>
</navigation>

When your MainActivity started, just do the navigation with action id, it will remove fragmentA in the stack, and jump to fragmentB. Seemingly, fragmentB is your start destination.

if(!isAllSetUp)
{
  // FragmentB
  navController.navigate(R.id.action_a_to_b)
}