Algorithmic reasoning -- the ability to perform step-by-step logical inference -- has become a core benchmark for evaluating reasoning in graph neural networks (GNNs) and large language models (LLMs). Ideally, one would like to design a single model capable of performing well on multiple algorithmic reasoning tasks simultaneously. However, this is challenging when the execution steps of algorithms differ from one another, causing negative interference when they are trained together. We propose branching neural networks, a principled architecture for multitask algorithmic reasoning. Searching for the optimal $k$-ary tree with $L$ layers over $n$ algorithmic tasks is combinatorial, requiring exploration of up to $k^{nL}$ possible structures. We develop AutoBRANE, an efficient algorithm that reduces this search to $O(nL)$ time by solving a convex relaxation at each layer to approximate an optimal task partition. The method clusters tasks using gradient-based affinity scores and can be used on top of any base model, including GNNs and LLMs. We validate AutoBRANE on a broad suite of graph-algorithmic and text-based reasoning benchmarks. We show that gradient features estimate true task performance within 5% error across four GNNs and four LLMs (up to 34B parameters). On the CLRS benchmark, it outperforms the strongest single multitask GNN by 3.7% and the best baseline by 1.2%, while reducing runtime by 48% and memory usage by 26%. The learned branching structures reveal an intuitively reasonable hierarchical clustering of related algorithms. On three text-based graph reasoning benchmarks, AutoBRANE improves over the best non-branching multitask baseline by 3.2%. Finally, on a large graph dataset with 21M edges and 500 tasks, AutoBRANE achieves a 28% accuracy gain over existing multitask and branching architectures, along with a 4.5$\times$ reduction in runtime.