Dense embedding-based retrieval is now the industry standard for semantic search and ranking problems, like obtaining relevant web documents for a given query. Such techniques use a two-stage process: (a) contrastive learning to train a dual encoder to embed both the query and documents and (b) approximate nearest neighbor search (ANNS) for finding similar documents for a given query. These two stages are disjoint; the learned embeddings might be ill-suited for the ANNS method and vice-versa, leading to suboptimal performance. In this work, we propose End-to-end Hierarchical Indexing -- EHI -- that jointly learns both the embeddings and the ANNS structure to optimize retrieval performance. EHI uses a standard dual encoder model for embedding queries and documents while learning an inverted file index (IVF) style tree structure for efficient ANNS. To ensure stable and efficient learning of discrete tree-based ANNS structure, EHI introduces the notion of dense path embedding that captures the position of a query/document in the tree. We demonstrate the effectiveness of EHI on several benchmarks, including de-facto industry standard MS MARCO (Dev set and TREC DL19) datasets. For example, with the same compute budget, EHI outperforms state-of-the-art (SOTA) in by 0.6% (MRR@10) on MS MARCO dev set and by 4.2% (nDCG@10) on TREC DL19 benchmarks.