Because of the sins of the priesthood and the people, God wasn’t speaking to Israel. Scripture says, “And the word of the Lord was rare in those days; there was no widespread revelation” (1 Samuel 3:1, NKJV). In the middle of this famine of the Word, though, the Lord appeared to the young Samuel: “The Lord called Samuel [who] did not yet know the Lord, nor was the word of the Lord yet revealed to him” (1 Samuel 3:4, 7).
Samuel was only twelve years old, but he didn’t yet recognize the voice of the Lord. So God came to his bedside and spoke his name out loud. Samuel first thought Eli was speaking; he didn’t know he was being trained to discern voices, to hear directly from God!
God wasn’t speaking to Eli the priest who had grown deaf to his voice. In fact, it seems that only one prophet was hearing from God: the unnamed man who warned Eli that God was about to cut him off (see 1 Samuel 2:27-36).
Hearing from God takes more than quiet time alone, more than simply saying, “Speak, Lord, for your servant hears!” No, there is no formula for hearing God. Put simply, he speaks to those who have prepared their hearts to hear.
Samuel had no deep theological knowledge of God when the Lord first spoke to him, but he had a tender, pure, devoted heart that was open to the Lord. So what do you think was the first thing God taught him? He said, “I’m going to judge Eli because he knew his sons were wicked, but did nothing to restrain them. They should have been stripped of their robes and told, ‘You can’t go near the holy place.’ Therefore, Samuel, I‘m going to show you my hatred for sin in my house. I want to you to know what it takes to hear my voice and walk with me” (see 1 Samuel 3:11-14).
It's no wonder the Bible says Samuel spoke such sure words. He had heard the voice of the Lord! He spent much time shut in with God, praying and seeking him, and God spoke clearly to him each time.
There are people around the world who have been trained to know God’s voice. These praying saints pour out their hearts to him, and he pours himself out to them.