Encounters with Jesus: Nicodemus

March 1, 2026 homily on John 3:1-17 by Pastor Galen for the Second Sunday in Lent

“For God so loved the world that he gave his only Son, so that everyone who believes in him may not perish but may have eternal life.” – John 3:16

Questions at Night

When my brother and I were teenagers, my older brother Nathan had a habit that my parents probably remember very well.

Just when it was time to get ready for bed, when everyone was tired and the day was winding down, my brother Nathan would suddenly want to have long, deep philosophical discussions.

My dad, ready to finally get some rest after a long day at work, genuinely wanted to be supportive and listen to what he had to say. But he also wondered aloud why Nathan couldn’t start these conversations earlier in the day instead of right when it was time to go to bed

There’s something about nighttime that prompts deep thoughts for many of us, isn’t there?

Not everyone delivers long philosophical treatises in the evening like my brother, who is now, fittingly, a professor and a preacher. But for many of us, the deep thoughts come when we’re lying in bed trying to sleep. Our minds won’t settle. We ruminate. We worry. We ask ourselves questions.

And perhaps that’s why Nicodemus came to Jesus at night.

Nicodemus

Nicodemus was not just anyone. He was a Pharisee, a leader of the Jews, educated, respected, deeply religious, a teacher of Israel. He had devoted his life to studying Scripture and seeking God. He wasn’t a skeptic trying to trap Jesus. He wasn’t an outsider looking in. He was someone serious about faith.

And yet he still had questions. So he comes to Jesus at night. Maybe he didn’t want others to see him. Maybe he wasn’t sure what his colleagues would think if they saw him talking to Jesus. Or maybe nighttime was simply when he could finally slow down, when he could finally find quiet space to ask Jesus what was truly on his heart.

Nicodemus begins respectfully: “Rabbi, we know that you are a teacher who has come from God” (John 3:2). He recognizes something in Jesus. He senses that God is at work. But he doesn’t yet understand what that means.

And before Nicodemus even fully voices his question, Jesus answers the deeper question of his heart: “Very truly, I tell you, no one can see the kingdom of God without being born from above” (John 3:3), or in some translations, being born “again.”

A Confusing Answer

Nicodemus is baffled. “How can anyone be born after having grown old?” he asks. “Can one enter a second time into the mother’s womb?” (John 3:4). Nicodemus thought Jesus was speaking literally. Jesus is speaking spiritually. Nicodemus is thinking about starting life over. Jesus is talking about receiving new life.

Jesus explains: “What is born of the flesh is flesh, and what is born of the Spirit is spirit… The wind blows where it chooses… so it is with everyone born of the Spirit” (John 3:6–8). In other words, the life God offers is not self-improvement. It is not trying harder. It is not simply becoming more religious.

It is transformation. It is new birth. It is life shaped by the Spirit of God. It is not something we manufacture. It is something we receive.

Faith Is More Than Intellectual

Nicodemus responds honestly, asking, “How can these things be?” (John 3:9). And I love that question because it reveals humility. It shows honesty. It reveals someone willing to admit he doesn’t understand.

Nicodemus was intelligent. Learned. Spiritually serious. And yet even he could not grasp what Jesus was saying. And maybe that’s part of the point.

Faith is not anti-intellectual. But it certainly goes beyond intellectual understanding. We cannot reason our way into new birth. We cannot control the Spirit. We cannot engineer transformation. We can only receive what God gives.

The Heart of the Gospel

Then Jesus moves to the heart of the message. He speaks of the Son of Man being lifted up, pointing toward his impending death on the cross. And then come the words many of us know by heart: “For God so loved the world that he gave his only Son, so that everyone who believes in him may not perish but may have eternal life” (John 3:16).

Notice that Jesus does not say that God so loved the worthy. He does not say God so loved the righteous. He does not say God so loved the people who had everything figured out.

God so loved the world. And Jesus continues: “Indeed, God did not send the Son into the world to condemn the world, but in order that the world might be saved through him” (John 3:17). The new birth Jesus speaks about flows from love. Not condemnation, but salvation. Not shame, but grace.

To be born from above is to live in the reality that we are deeply loved by God.

Born from Above

So what does this mean for us? I think Nicodemus’ encounter with Jesus demonstrates being born from above is not always a dramatic emotional moment. It is not about spiritual superiority. It is not checking the right religious boxes. 

It is a reoriented life. A softened heart. A new way of seeing the world. A new identity shaped by the Spirit. It is learning to trust God more deeply, to love more freely, to live more fully in the light of Christ. It is God doing something new within us, sometimes suddenly, but more often gradually, and always by grace.

And if we’re honest, many of us are more like Nicodemus than we realize. We have questions. We live with uncertainty. We come seeking understanding. Maybe those questions come at night, in quiet moments of worry, in seasons of change, in times of doubt, in moments when life feels uncertain.

And Jesus meets us there. Not with condemnation, but with an invitation. Not with rejection, but with new life.

Later in John’s Gospel, Nicodemus speaks up in Jesus’ defense. And after Jesus is crucified, Nicodemus helps prepare his body for burial, bringing costly spices and stepping into the open. Its fascinating that the one who first came to Jesus under the cloak of darkness finally steps into the light.

An Invitation

Sometimes encounters with Jesus do not produce immediate, visible change. Transformation is often gradual. New birth is a journey.

And so there is something deeply encouraging to me about Nicodemus’ story. He does not leave that conversation with everything figured out. He leaves with mystery. He leaves with questions. He leaves with an invitation. And sometimes that is exactly where faith begins.

We don’t always see the moment when God begins something new in us. We don’t always recognize when the Spirit starts moving. We don’t always feel transformed overnight. Sometimes new birth begins quietly, in a question that we just can’t shake, in a longing that we can’t explain, or in a restlessness that tells us there must be something more.

There’s a story about a man who planted bamboo in his garden. He watered it faithfully. He tended the soil. He waited.

The first year, nothing appeared above the surface. The second year, still nothing. The third year, there was still nothing. And even in the fourth year there was no visible growth.

Most people in that situation would give up, assuming nothing was going to happen. But underground, something was happening all along.

Roots were spreading. Depth was forming. Strength was developing. All in the dark, below the surface. 

Then in the fifth year, almost suddenly, the bamboo shot up, rising nearly ninety feet in just a matter of weeks! The growth that seemed sudden had actually been years in the making.

Similarly, Nicodemus came to Jesus at night. In the dark. With questions he did not fully understand. And it seems that he left still somewhat confused. He didn’t walk away instantly transformed. But something had been planted. A root of courage, perhaps. A root of curiosity. A root of faith. And later — much later — when the other disciples had scattered, Nicodemus stepped into the light. The one who first came in secret now stood in the open. What was growing underneath the surface eventually became visible.

And maybe that is what Jesus meant by being born from above. New birth does not always look dramatic. Sometimes it looks like quiet rooting. Sometimes it looks like unseen growth. Sometimes it looks like questions asked in the night.

And maybe some of you are in that kind of season right now. You don’t see dramatic change. You don’t feel spiritually “tall.” You don’t feel fully certain. But that does not mean God is not at work. Roots grow in the dark. The Spirit moves where we cannot see. God shapes us beneath the surface. Grace carves depth in the quiet places.

Nicodemus came to Jesus at night. And in that darkness, something began.

Maybe this season of your life is not the end of your faith story. Maybe it is the beginning of deeper roots.

The God who watches over your going out and your coming in, the God who keeps you, the God who loves the world, is even now making you new.

So come honestly. Come with your questions. Come with your uncertainty. Come to Jesus just as you are, and allow yourself to be born from above.

Amen.

Questions for Personal Reflection in Response to today’s message:

  1. What questions or concerns tend to surface for you in the “night seasons” of your life?
  2. Where might you be seeking deeper understanding or new life right now?
  3. Where might God be at work in your life beneath the surface, even if you cannot see visible change?
  4. What might it look like for you to come honestly to Christ with your questions this week?
  5. Where do you sense the Spirit inviting you toward growth, renewal, or deeper trust?

Published by Galen Zook

I am an artist, preacher, minister, and aspiring theologian