We initiate the study of quantum agnostic learning of phase states with respect to a function class $C \subseteq {c:{0,1}^n\rightarrow {0,1}}$: given copies of an unknown $n$-qubit state $|\psi⟩$ which has fidelity $\textsf{opt}$ with a phase state $|\phi_c⟩=\frac{1}{\sqrt{2^n}}\sum_{x\in {0,1}^n}(-1)^{c(x)}|x⟩$ for some $c\in C$, output $|\phi⟩$ which has fidelity $|⟨\phi | \psi ⟩|^2 \geq \textsf{opt}-\varepsilon$. To this end, we give agnostic learning protocols for the following classes: 1. Size-$t$ decision trees which runs in time $\textsf{poly}(n,t,1/\varepsilon)$. This also implies $k$-juntas can be agnostically learned in time $\textsf{poly}(n,2^k,1/\varepsilon)$. 2. $s$-term DNF formulas in time $\textsf{poly}(n,(s/\varepsilon)^{\log \log (s/\varepsilon) \cdot \log(1/\varepsilon)})$. Our main technical contribution is a quantum agnostic boosting protocol which converts a “weak” agnostic learner, which outputs a parity state $|\phi⟩$ such that $|⟨\phi|\psi⟩|^2\geq \textsf{opt}/\textsf{poly}(n)$, into a “strong” learner which outputs a superposition of parity states $|\phi’⟩$ such that $|⟨\phi’|\psi⟩|^2\geq \textsf{opt} - \varepsilon$. Using quantum agnostic boosting, we give a $n^{O(\log(n/\varepsilon)\cdot \log \log n)}$-time algorithm for $\varepsilon$-learning $\textsf{poly}(n)$-sized depth-$3$ circuits (consisting of $\textsf{AND}$, $\textsf{OR}$, $\textsf{NOT}$ gates) in the uniform $\textsf{PAC}$ model given quantum examples. Classically, obtaining an algorithm with a similar complexity has been an open question in the $\textsf{PAC}$ model and our work answers this given quantum examples.