Intro to Java - determine valid unique numbers
It looks alright, but there are some improvements you can do. First of all, you can still split your program into smaller functions still, which really helps readability. 

Also, something glaring to me is that your functions in "main" are acting as instance variables for the rest of the class, which should not be the case. You should choose where you declare your variables based on the necessity of their scope. If you only use the input int as a store from user input, it should only be declared in the method that gets input from the user.

For instance, you could omit the input int from main and declare it locally in the GetInputFromUser method.

In main:

for (int i = 0; i &lt; validNumber.length; i++) {
     GetInputFromUser(validNumber, uniqueNumber);
}


The method:

public static void GetInputFromUser(int[] validNums, int[] uniqueNums) {
     int input = userInput.nextInt()
     while (!isValid(input)) {
          System.out.print("\nEnter an integer: \t");
          input = userInput.nextInt();
     }
     //Code ommitted

}


I didn't really have time to read all of the specifications carefully, but I hope this helped a bit! Also, you may want to declare the int arrays as instance variables to avoid passing them around all the time.