“Now then, your two sons born to you in Egypt before I came to you here will be reckoned as mine; Ephraim and Manasseh will be mine, just as Reuben and Simeon are mine. Any children born to you after them will be yours; in the territory they inherit they will be reckoned under the names of their brothers. As I was returning from Paddan, to my sorrow Rachel died in the land of Canaan while we were still on the way, a little distance from Ephrath. So I buried her there beside the road to Ephrath” (that is, Bethlehem). When Israel saw the sons of Joseph, he asked, “Who are these?”
Genesis‬ 48‬:5‬-8‬ NIV‬‬

”But Israel reached out his right hand and put it on Ephraim’s head, though he was the younger, and crossing his arms, he put his left hand on Manasseh’s head, even though Manasseh was the firstborn.“
Genesis‬ 48‬:14‬ NIV‬‬

So… we keep seeing this trend again and again, the second born is blessed above or over the first. There is Isaac over Ishmael, Jacob over Esau, and now Ephraim over Manasseh. Seems like the firstborn are just simply not catching a break. What’s the deal with the second son?

Initially we see Jacob claiming Ephraim and Manasseh as his own sons, so before we understand the blessing being conferred on them, we need to look at this claim. In Jewish culture, the blessing of the firstborn is an essential and revered thing. The first born is to receive the birthright; a consecration to the Lord.
”You are to give over to the Lord the first offspring of every womb. All the firstborn males of your livestock belong to the Lord.“
Exodus‬ 13‬:12‬ NIV‬‬

This conferred certain rights, responsibilities, and privileges to the firstborn. However, because of the sins of Ruben, Simeon, and Levi, Jacob (also known as Israel) claims the sons of Joseph and confers on them the blessing instead. In doing so, he elevates Joseph - now Joseph is represented twice amongst the tribes of Israel. Instead of the establishment of a tribe of Joseph, different tribes are established from the names of each of his sons. Through this blessing, Israel is confirming the call and leading of God in Joseph’s life.
Of all his sons it is Joseph that demonstrates a life lived in worship to God.

So now that Ephraim and Manasseh have been spiritually adopted as Israel’s sons, he proceeds to bless them as such. He, however, proceeds to bless the younger over the older. Why? When we look at the perception at the time of their birth we might understand...

”Joseph named his firstborn Manasseh and said, “It is because God has made me forget all my trouble and all my father’s household.”“
Genesis‬ 41‬:51‬ NIV‬‬

Joseph here sees Manasseh as a son born to him so as to heal from the hurts he has experienced in his life. It’s as if in Manasseh he comes to terms or accepts that he no longer was a part of his father’s household. He assumes the position that this is his life now and his life now is a far cry from the life he knew while in Israel’s care. This disassociation can be seen as cutting himself off from the blessing that would come through his father - a worldly perspective, similar to how Ishmael was born from a worldly compromise and it was not through him that God’s blessing of Abraham would be carried.

Of the birth of Ephraim he says;

”The second son he named Ephraim and said, “It is because God has made me fruitful in the land of my suffering.”
Genesis‬ 41‬:52‬ NIV‬‬

In Ephraim, Joseph sees fruitfulness. The blessing of the firstborn is that of first fruit.
As he spoke this, while naming his second son, he was in a sense being prophetic as God himself would later declare:

”They will come with weeping; they will pray as I bring them back. I will lead them beside streams of water on a level path where they will not stumble, because I am Israel’s father, and Ephraim is my firstborn son.“
Jeremiah‬ 31‬:9‬ NIV‬‬

God seems to use the first to reveal the corruptible, a picture of how the first covenant revealed the level required by God for holiness - thus revealing corruptible man. Through the second covenant of Christ, we find the redemption for mankind. It seems that God is in the business of selecting the least to confound the big or wise.

One last note: Joseph is considered a type of Christ. In Joseph’s life we see a foreshadowing of the grafting in of the Gentiles, in through his own sons is the introduction of foreign blood (by Joseph’s wife). Are we, too, not a type of second son?

For further study:
Holy Land Illustrated Bible (CSB)