Matthew 3:11 I indeed baptize you with water unto repentance. but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Ghost, and with fire.
Luke 3:16 John answered, saying unto them all, I indeed baptize you with water; but one mightier than I cometh, the latchet of whose shoes I am not worthy to unloose: he shall baptize you with the Holy Ghost and with fire:
Mark 1:8 I Indeed have baptized you with water, but He will baptize you with the Holy Spirit.
John 1:33 And I knew him not: but he that sent me to baptize with water, the same said unto me, Upon whom thou shalt see the Spirit descending, and remaining on him, the same is he which baptizeth with the Holy Ghost.
Notice what John says: The baptism of the Holy Spirit is different and better than the baptism with water; and second that someone else not himself (John) will baptize you with the Holy Spirit and with fire. At the time John said these things He did not know who would do this. He did not know it would be Jesus. John only knew that he himself was sent by God to baptize with water and prepare the way of the Lord. Notice too that John the baptizer says that it was God who told him that someone else would come and baptize people with the Holy Spirit.
Matthew 20:22,23 But Jesus answered and said, "You do not know what you ask. Are you able to drink the cup that I am about to drink, and be baptized with the baptism that I am baptized with?" They said to Him, "We are able." So He said to them, "You will indeed drink My cup, and be baptized with the baptism that I am baptized with; but to sit on My right hand and on My left is not Mine to give, but it is for those for whom it is prepared by My Father."
Mark 10:38,39 But Jesus said to them, "You do not know what you ask. Are you able to drink the cup that I drink, and be baptized with the baptism that I am baptized with?" They said to Him, "We are able." So Jesus said to them, "You will indeed drink the cup that I drink, and with the baptism I am baptized with you will be baptized; but to sit on My right hand and on My left is not Mine to give, but it is for those for whom it is prepared."
The Book of Acts
Acts 1:4,5 And being assembled together with them, He commanded them not to depart from Jerusalem, but to wait for the Promise of the Father, "which," He said, "you have heard from Me; for John truly baptized with water, but you shall be baptized with the Holy Spirit not many days from now."
Acts 1:8 But you shall receive power when the Holy Spirit has come upon you; and you shall be witnesses to Me in Jerusalem, and in all Judea and Samaria, and to the end of the earth."
Acts 2:1-4 When the Day of Pentecost had fully come, they were all with one accord in one place. And suddenly there came a sound from heaven, as of a rushing mighty wind, and it filled the whole house where they were sitting. Then there appeared to them divided tongues, as of fire, and one sat upon each of them. And they were all filled with the Holy Spirit and began to speak with other tongues, as the Spirit gave them utterance.
Acts 8:14-21 Now when the apostles who were at Jerusalem heard that Samaria had received the word of God, they sent Peter and John to them, who, when they had come down, prayed for them that they might receive the Holy Spirit. For as yet He had fallen upon none of them. They had only been baptized in the name of the Lord Jesus. Then they laid hands on them, and they received the Holy Spirit. And when Simon saw that through the laying on of the apostles’ hands the Holy Spirit was given, he offered them money, saying, "Give me this power also, that anyone on whom I lay hands may receive the Holy Spirit." But Peter said to him, "Your money perish with you, because you thought that the gift of God could be purchased with money! You have neither part nor portion in this matter, for your heart is not right in the sight of God."
Acts 11:16 At that very moment, three men stood before the house where I was, having been sent to me from Caesarea. Then the Spirit told me to go with them, doubting nothing. Moreover these six brethren accompanied me, and we entered the man’s house. And he told us how he had seen an angel standing in his house, who said to him, ‘Send men to Joppa, and call for Simon whose surname is Peter, who will tell you words by which you and all your household will be saved.’ And as I began to speak, the Holy Spirit fell upon them, as upon us at the beginning. Then I remembered the word of the Lord, how He said, ‘John indeed baptized with water, but you shall be baptized with the Holy Spirit.’ If therefore God gave them the same gift as He gave us when we believed on the Lord Jesus Christ, who was I that I could withstand God?" When they heard these things they became silent; and they glorified God, saying, "Then God has also granted to the Gentiles repentance to life."
Ephesians 4:4-6 There is one body and one Spirit, just as you were called in one hope of your calling; one Lord, one faith, one baptism; one God and Father of all, who is above all, and through all, and in you all. (Baptism here is not water baptism which is symbolic of the new birth, but it is the baptism of the Holy Spirit - the one baptism.)
Hebrews 6:1,2 Therefore, leaving the discussion of the elementary principles of Christ, let us go on to perfection, not laying again the foundation of repentance from dead works and of faith toward God, of the doctrine of baptisms, of laying on of hands, of resurrection of the dead, and of eternal judgment. ("Baptisms" plural refers to John's baptism of repentance, water baptism and the baptism of the Spirit.)
Based on the above verses we see that the baptism of the Holy Spirit is administered by the laying on of hands and through the speaking of the word of God. In the Bible it is recorded that all this took place through the apostles. Nowhere does it say that Paul the apostle was baptized in the Holy Spirit however this could be what happened when Jesus appeared to him on his trip to Damascus. Also nowhere in scripture does it mention that Stephen "a man full of faith and the Holy Spirit" was baptized in the Spirit; however, this lack of mention does not mean that he wasn’t. I mention him because he was not an apostle yet he did many miracles and signs.
A lot of Christians say that being filled with the Holy Spirit is the same thing as being baptized with the Holy Spirit. If we compare water baptism with Spirit baptism then we will see that that simply is not true. If you drink a lot of water, at some point you could say "I am filled with water," but that would not be the same thing as being immersed into water would it. On the other hand if you were to be immersed into water you would not say "I am filled with water" would you. Using this comparison of water to show the difference between immersion and being filled we can easily see the difference. Being filled means that the water is inside you to a great degree. Being immersed means that you are inside the water to a great degree. Being filled means that a large amount of water is inside you. Being immersed means that you are inside a large amount of water. So it is with the Spirit. What actually happens though when a person is baptized into the Holy Spirit is that they are also filled at the same time. But you can be filled with the Holy Spirit without being immersed into the Holy Spirit just as you can drink a lot of water without being immersed into the water. So you see being filled is one thing being immersed is another, they are two completely different things. Remember, John said Jesus would baptize with the Holy Spirit. Jesus said he would, and the apostles did baptize people in the Holy Spirit. Yes people are still baptized in the Holy Spirit today. Let go of your traditions and believe what God says in his word and seek to know him fully.
One of the reasons a lot of Christians resist the baptism of the Holy Spirit is because they resist the idea of speaking in tongues which has been proclaimed as accompanying the baptism of the Holy Spirit (which is not necessarily the case.) In general most Christians who resist the baptism of the Holy Spirit also resist the gifts of the Spirit and vice versa. They resist the gifts and they resist the Baptism also. I know of seven men who used to belong to a particular denomination. When they were baptized into the Holy Spirit and began to experience the gifts of the Spirit eventually they left their denomination. They simply could not have fellowship with others who were continually resisting the Holy Spirit. If you have not been baptized in the Holy Spirit, I would encourage you to seek the Lord in preparation and seek to be baptized in the Holy Spirit.