The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40S ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNASec) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria. In all domains of life, the essential trace element selenium is incorporated into selenoproteins as the amino acid selenocysteine during protein translation. Specialized protein and RNA factors assist selenocysteine transfer RNA to reinterpret specific UGA codons, not as a signal to end protein synthesis, but rather as a sign for selenocysteine insertion. Hilal et al. used cryo–electron microscopy to trap and visualize the mammalian ribosome as it decodes the selenocysteine UGA codon. An unforeseen extended network of interactions between key molecular players facilitates the recoding event, thereby providing a basis for further studies of this fundamental biological process. —DJ Visualization of selenoprotein elongation in eukaryotes is described.