Paul's “thorn in the flesh" is the next most common objection to divine healing to be raised after the issue of Job. It is claimed that Paul's thorn in the Flesh was a sickness that God didn't want to heal him from, but gave him the strength to bear. We should therefore also accept sickness in our lives as a thorn in our flesh that God doesn't always remove. When we study the text, however, we see that this is not about sickness at all.
So to keep me from becoming conceited because of the surpassing greatness of the revelations, a thorn was given me in the flesh, a messenger of Satan to harass me, to keep me from becoming conceited. Three times I pleaded with the Lord about this, that it should leave me. ' But he said to me, "My grace is sufficient for you, for my power is made perfect in weakness." Therefore I will boast all the more gladly of my weaknesses, so that the power of Christ may rest upon me.
For the sake of Christ, then, I am content with weaknesses, insults, hardships, persecutions, and calamities. For when I am weak, then I am strong.
The story of Paul's thorn in the flesh is actually really easy to explain.
Firstly, this thorn in the flesh didn't come from God but from satan. Paul himself says exactly what his thorn is: "An angel of satan, to harass me or literally’ strike me with fists’." The origin of the thorn was not God, but an angel of satan. Even if the thorn was a sickness (which it isn’t) it’s satan who makes people sick, not God.
Secondly, we know that Paul's thorn had nothing to do with sicknes at all. Paul says it was an angel of satan. The creek word translated as angel here, aggelos, can also be translated as "messenger." The thorn in Pauls flesh was a messenger from Satan, who struck him with its fists. "Struck him with its fists" doesn't indicate sickness, but physical persecution.
Paul literally took punches. Paul used exactly the same phrase when talking to the Corinthians earlier: "To the present hour we … are … beaten" (1 Corinthians 4:11).
Why was Paul so persecuted? Because of the revelations that He had received (1 Corinthians 4:7). This opposition tried to stop Paul and work against him. Paul had tremendous revelations about Jesus: that He came to save both Jews and Gentiles alike. That was the great mystery entrusted to Paul. It is because of his mesage, that God also has mercy on Gentiles, and we can be saved just by grace and faith, that Paul experienced enormous persecution. This manifested itself in opposition, such as physical violence and torture and false. teachers who tried to invalidate his message. When Paul spoke of his revelations in the letter to the Ephesians, he also said that that was the reason for his opposition.
1 For this reason I, Paul, the prisoner of Christ Jesus for you Gentiles—
3 …how that by revelation He made known to me the mystery (as I have briefly written already,
6 that the Gentiles should be fellow heirs, of the same body, and partakers of His promise in Christ through the gospel,
Paul devoted himself to the Gospel and was persecuted a lot. That’s why Paul says:
…a thorn in the flesh was given to me, a messenger of Satan to buffet me, lest I be exalted above measure. Concerning this thing I pleaded with the Lord three times that it might depart from me. And He said to me, “My grace is sufficient for you, for My strength is made perfect in weakness.” Therefore most gladly I will rather boast in my infirmities, that the power of Christ may rest upon me. Therefore I take pleasure in infirmities, in reproaches, in needs, in persecutions, in distresses, for Christ’s sake. For when I am weak, then I am strong.
Take a good look at what it says here. First off, Paul said that a thorn in the flesh was given him. Then Paul said that he had asked God to take it away, but God told him that His grace is enough, because His grace is made perfect in weakness. God's power was visible because of the weakness, Paul's thorn in the flesh. Paul then listed what he meant by "thorn in the flesh"; "weaknesses, insults, hardships, persecutions, and calamities" (2 Corinthians 12:10, ESV). It's unbelievable that theologians have already spent years discussing what Paul's thorn in the flesh was, when Paul literally told us exactly what it was in the very next verse!
Paul was dealing with persecution. Paul went on with what he was talking about before this, in Chapter 11. This is where he listed even more persecution that he had had to deal with. Paul mentioned in 2 Corinthians 11:23 that he had suffered from beatings, imprisonment, danger of death, whipping, scourging with rods, stoning and being shipwrecked, not to mention being endangered by robbers, fellow citizens, heathens, and false teachers, and so on. Paul listed all kinds of problems that he had had to deal with, but he never mentioned sickness. The term "thorn" is also used a fair bit in the Old Testament.
Paul knew the Old Testament very well and Paul chose the term "thorn" for a reason. A thorn is never linked to sickness in the Old Testament, but to persecution and opposition (Numbers 33:55, Joshua 23:13 and Ezekiel 2:6). From these texts we can deduce that Israel's "thorn in the flesh" was the nations who fought and oppressed them because they disobeyed God's command. Paul's thorn in the flesh was persecution and opposition. This also explains why God gave Paul the grace to bear it, because we are all promised opposition and persecution, just as people persecuted Christ (Matthew 10:25, 2 Timothy 3:12, John 15:18 and1 Peter 4:12).
So, Paul's thorn in the flesh was all kinds of persecution, abuse and opposition that atempted to keep him from spreading the Gospel. Paul asked God to take it away, but God told him that the opposition would continue. God would be glorified in the midst of the persecution and opposition.