What to do with intrusive thoughts

I understand what it's like to have thoughts that scare you. Thoughts that disturb and disrupt and make you doubt.

Our minds are mysterious and complex. They generate 6,000 thoughts per day on average. Many of those thoughts are considered automatic—meaning they arise out of the subconscious mind, rather than being conscious or chosen—and approximately 80% of those thoughts tend to be negative.

Sometimes a thought appears that is so disturbing, so very against what you consciously believe, desire, or hold dear, that its very existence makes you tremble.

I’ve had thoughts like this since I was little. Sometimes these thoughts have come in the form of doubts and “what if’s”—whether my Mom would make it home from the grocery store, whether I’d die of a heart attack, make the wrong decision, marry the wrong person, was in the wrong body, whether I’d be killed, end my own life, get sick from the chicken I just ate, and endless other frightening possibilities. Other times, scary thoughts have come in the form of statements—disturbing declarations I don’t agree with and desperately don’t want in my brain.

For many years, I argued with these thoughts. I tried to defend myself against them. I tried to silence them. I tried to figure them out. I believed them. I tried to suppress them. I did whatever I could in my own strength, and it was…well, it was ineffective. Even counterproductive. The fear, the trembling, the terrifying thoughts only ever got worse.

It took me a very long time to learn this lesson: When our thoughts scare us, the Lord alone is mighty to save. Our ways won’t suffice.

His Word holds the answers and the truth that sets us free. That has and is setting me free. My hope here is to share some of that truth with you. This is what to do with intrusive thoughts.

What God says about our thoughts

  • His Word tells us that our thoughts do matter, but they don’t matter as much as his thoughts. We should be mindful not to undervalue or overvalue our thoughts.

  • His Word tells us that our thoughts are naturally rebellious, and that our minds need renewing. We can expect rebellious, at times disturbing, thoughts as we are renewed in Christ.

  • His Word tells us that letting our sinful nature control our minds leads to death, but letting the Holy Spirit control our minds brings life. We don’t have to let our old nature, and the rebellious thoughts that come with it, control our minds when we are in Christ.

Tending to your fear first

We will talk about how to let the Spirit control your mind. But first, when we feel very afraid, our brains and bodies go into a ‘fight or flight’ state and the part of our brains that can think rationally is not immediately accessible. When this is the case, we may not be able to logically look at our thoughts right away and need to tend to our fear first.

We don’t have power to control how automatically frightened we feel in the face of certain thoughts. We live in “bod[ies] of death” that often fear more than they need to (Romans 7:24). But while we cannot control every fearful feeling, we are instructed on what to do with our fear when it arises.

We are invited to “cast all our anxieties on him, because he cares” for us (1 Peter 5:7). We can go to God when we feel afraid of our thoughts. Rather than abide in them, we are invited to abide in him.

Philippians 4:6-7 outlines one way we can do this, telling us to “pray about everything” that might cause us to worry. “Tell God what you need, and thank him for all he has done. Then you will experience God’s peace, which exceeds anything we can understand.” Studies prove that this advice is aligned with how God created us. We physically cannot feel intensely afraid and deeply grateful at the same time!

Another way to “go to God” is to turn to a sister or brother in Christ for help carrying the burden of our fear. He gave us one another. When we are feeling afraid, we can turn to and tell someone we trust. They can listen to us, give us a hug if we need one, pray for us, and/or encourage us with the truth. They can be an in-person representative of the God who cares for us and isn’t afraid like we are in that moment.

Letting the Holy Spirit control your mind

Now that you’re regulated and able to think clearly, it’s time to talk about how to let the Spirit, not our sinful nature, control our minds.

We don’t have the power to control every single thought that enters our minds, but we are instructed on what to do with our naturally rebellious thoughts.

First, we are told to fix our thoughts on “what is true, and honorable, and right, and pure, and lovely, and admirable…things that are excellent and worthy of praise” (Philippians 4:8). We get to choose what we focus on. Our sinful nature wants us to focus on what is untrue or uncertain, dishonorable, impure, or unlovely. This can include focusing on our disturbing thoughts. We are tempted to fix our gaze elsewhere, but we have been given the power in Christ to focus on what is true—the source and fullness of which is Jesus. We can practice focusing our minds on him, his Word, and the real, praise-worthy evidence of his goodness, glory, and power all around us.

Secondly, we are called to “capture rebellious thoughts and teach them to obey Christ” (2 Corinthians 10:5). When a thought is frightening or disturbing, we need to hold it up against Scripture and what is true. We don’t take our thoughts as fact, and we don’t try to suppress them. Rather, we seek wisdom from God and teach our thoughts to submit to Christ - the truth.

One of the things I’ve personally learned in this process is not to concern myself with “matters too great or too awesome for me to grasp” (Psalm 131:1). God’s thoughts and ways are higher than mine—I do not know or understand everything. Sometimes a scary thought tempts us to concern ourselves with something “too great” for us, such as exact details about the past, present, or future that may not be for us to know. When this is the case, obeying Christ looks like allowing for mystery and uncertainty—trusting God alone to be God—which “calms and quiets” our souls (Psalm 131:2).

His grace is sufficient for you

Your thoughts may scare you, but you don’t have to be alone with your fear. Your thoughts may scare you, but you don’t have to stay afraid of them.

If there is any ounce of truth in them, rest assured that it is not the whole truth. Perfect love casts out fear, it doesn’t abandon us in it.

We have not been left without instruction. We have not been left without comfort. We have not been left without sufficient grace in Jesus Christ to cover us completely—terrible and terrifying thoughts included. His grace is sufficient for us.

Rather than tremble alone in fear, we can turn to God or one of His children and tell them we’re afraid. Rather than fix our gaze on our scary thoughts, we can fix our gaze on him who died for us, and on all the ways he is caring for us. Rather than believe our thoughts, we can lovingly correct anything that doesn’t align with the truth of his Word and the Gospel. As we do this, remaining in his love, our minds will be renewed and we will be transformed, knowing more and more of the truth.

We may even find, as we humbly deal with our scary thoughts and feelings of fear his way, that they did not arise for nothing, but were part of God’s perfect treatment plan to heal us, humble us, and draw us closer to himself. That is my story. At the very least, we can trust that he uses them for that purpose—he never wastes our suffering, but uses it for our good as we trust in him.

And one day, every ugly, unwanted thought, every terrible, scary feeling, every bit of suffering, will be washed away as he makes all things new.

It will not always be this way.

Go to God in prayer

You can use the following prayer to go to God when you feel afraid:

Lord, I am feeling (insert a feeling word to describe how you’re feeling—ex. afraid, anxious, overwhelmed, uncertain.) Would you give me (insert what you’re needing relationally from him—ex. reassurance, encouragement, wisdom, comfort)? Thank you for listening to my prayer. Thank you for all the ways you provide for my needs, (insert specific examples of how God has cared for you in the past or ways you see him caring and providing for you in the present—ex. for covering all of my thoughts and sin with your grace)...

Continue to tell him what you’re thankful for. Allow yourself to be specific, and to deeply acknowledge and feel the evidence of God’s presence and care for you.

Practice capturing rebellious thoughts

When you’re ready, you can use the following reflection questions to examine your scary thoughts. Choose one thought and answer the following questions:

  • Is this thought aligned with Scripture? With the gospel?

  • Are there any relevant facts this thought is ignoring?

  • Does this thought concern something that may be “too great” for me?

  • What am I afraid of when I have this thought?

  • Is my fear aligned with the truth? With the gospel?

  • Does my fear account for the greatness and goodness of God?


If you would like to work with a professional counselor on issues related to anxiety or intrusive, scary thoughts and you are a California resident, you can learn more about my virtual and in-person (Orange County only) counseling services here.

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