Small noncoding RNAs play critical regulatory roles in development across organisms. This study profiled microRNAs (miRNAs) and tRNA-derived fragments (tRFs) during bovine conceptus elongation. Elongating conceptuses were obtained via superovulation of eight Angus heifers. Twenty samples from ovoid (OV, n = 6; 0.5–3 mm), tubular (TUB, n = 7; 5–15 mm), and filamentous (FIL, n = 7; 20–34 mm) stages underwent small RNA sequencing. Differential expression of miRNAs and tRFs was analyzed using DESeq2, accounting for donor-sire effects. No tRFs showed differential abundance across any pairwise comparisons. For miRNAs, the expressions of six miRNAs were upregulated in OV versus TUB conceptuses (padj < 0.05), including four let-7 family members (bta-let-7g, bta-let-7f, bta-let-7a-5p, and bta-let-7c) and two additional miRNAs (bta-miR-224 and bta-miR-449a). Furthermore, there were 3 miRNAs differently abundant between the ovoid and filamentous transition (padj < 0.04), including two members of the let7 family (bta-let-7g and bta-let-7f) and bta-miR-449a. Predicted targets of these differentially abundant miRNAs were identified using miRanda. Enrichment analyses of the targeted genes included pathways regulating cellular proliferation, pathways in cancer, and immune-related pathways. The let-7 family, along with miR-449a and miR-224, are candidate regulators of the balance between cellular proliferation and differentiation during elongation, based on their differential abundance and in silico target predictions.