diff --git a/res/css/views/emojipicker/_EmojiPicker.scss b/res/css/views/emojipicker/_EmojiPicker.scss
index 50eeb4281c..370ed561c5 100644
--- a/res/css/views/emojipicker/_EmojiPicker.scss
+++ b/res/css/views/emojipicker/_EmojiPicker.scss
@@ -57,10 +57,10 @@ limitations under the License.
         background-color: $focus-bg-color;
         border-bottom: 2px solid $button-bg-color;
     }
+}
 
-    .mx_EmojiPicker_anchor_selected {
-        border-bottom: 2px solid $button-bg-color;
-    }
+.mx_EmojiPicker_anchor_visible {
+    border-bottom: 2px solid $button-bg-color;
 }
 
 .mx_EmojiPicker_search {
diff --git a/src/components/views/emojipicker/Category.js b/src/components/views/emojipicker/Category.js
index 629dd3e570..dcda106719 100644
--- a/src/components/views/emojipicker/Category.js
+++ b/src/components/views/emojipicker/Category.js
@@ -30,7 +30,7 @@ class Category extends React.PureComponent {
     };
 
     render() {
-        const { onClick, onMouseEnter, onMouseLeave, emojis, name, filter } = this.props;
+        const { onClick, onMouseEnter, onMouseLeave, emojis, name } = this.props;
         if (!emojis || emojis.length === 0) {
             return null;
         }
diff --git a/src/components/views/emojipicker/EmojiPicker.js b/src/components/views/emojipicker/EmojiPicker.js
index d1f784f062..74864d1cee 100644
--- a/src/components/views/emojipicker/EmojiPicker.js
+++ b/src/components/views/emojipicker/EmojiPicker.js
@@ -71,8 +71,6 @@ class EmojiPicker extends React.Component {
             previewEmoji: null,
         };
 
-        this.bodyRef = React.createRef();
-
         this.recentlyUsed = recent.get().map(unicode => DATA_BY_EMOJI[unicode]);
         this.memoizedDataByCategory = {
             recent: this.recentlyUsed,
@@ -83,49 +81,92 @@ class EmojiPicker extends React.Component {
             id: "recent",
             name: _t("Frequently Used"),
             enabled: this.recentlyUsed.length > 0,
+            visible: true,
+            ref: React.createRef(),
         }, {
             id: "people",
             name: _t("Smileys & People"),
             enabled: true,
+            visible: true,
+            ref: React.createRef(),
         }, {
             id: "nature",
             name: _t("Animals & Nature"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "foods",
             name: _t("Food & Drink"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "activity",
             name: _t("Activities"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "places",
             name: _t("Travel & Places"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "objects",
             name: _t("Objects"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "symbols",
             name: _t("Symbols"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }, {
             id: "flags",
             name: _t("Flags"),
             enabled: true,
+            visible: false,
+            ref: React.createRef(),
         }];
 
+        this.bodyRef = React.createRef();
+
         this.onChangeFilter = this.onChangeFilter.bind(this);
         this.onHoverEmoji = this.onHoverEmoji.bind(this);
         this.onHoverEmojiEnd = this.onHoverEmojiEnd.bind(this);
         this.onClickEmoji = this.onClickEmoji.bind(this);
         this.scrollToCategory = this.scrollToCategory.bind(this);
+        this.updateVisibility = this.updateVisibility.bind(this);
 
         window.bodyRef = this.bodyRef;
     }
 
+    updateVisibility() {
+        const rect = this.bodyRef.current.getBoundingClientRect();
+        for (const cat of this.categories) {
+            const elem = this.bodyRef.current.querySelector(`[data-category-id="${cat.id}"]`);
+            if (!elem) {
+                cat.visible = false;
+                cat.ref.current.classList.remove("mx_EmojiPicker_anchor_visible");
+                continue;
+            }
+            const elemRect = elem.getBoundingClientRect();
+            const y = elemRect.y - rect.y;
+            const yEnd = elemRect.y + elemRect.height - rect.y;
+            cat.visible = y < rect.height && yEnd > 0;
+            // We update this here instead of through React to avoid re-render on scroll.
+            if (cat.visible) {
+                cat.ref.current.classList.add("mx_EmojiPicker_anchor_visible");
+            } else {
+                cat.ref.current.classList.remove("mx_EmojiPicker_anchor_visible");
+            }
+        }
+    }
+
     scrollToCategory(category) {
         const index = this.categories.findIndex(cat => cat.id === category);
         this.bodyRef.current.querySelector(`[data-category-id="${category}"]`).scrollIntoView();
@@ -141,6 +182,9 @@ class EmojiPicker extends React.Component {
             this.categories.find(cat => cat.id === id).enabled = this.memoizedDataByCategory[id].length > 0;
         }
         this.setState({ filter });
+        // Header underlines need to be updated, but updating requires knowing
+        // where the categories are, so we wait for a tick.
+        setTimeout(this.updateVisibility, 0);
     }
 
     onHoverEmoji(emoji) {
@@ -173,7 +217,7 @@ class EmojiPicker extends React.Component {
             <div className="mx_EmojiPicker">
                 <Header categories={this.categories} defaultCategory="recent" onAnchorClick={this.scrollToCategory}/>
                 <Search query={this.state.filter} onChange={this.onChangeFilter}/>
-                <div className="mx_EmojiPicker_body" ref={this.bodyRef}>
+                <div className="mx_EmojiPicker_body" ref={this.bodyRef} onScroll={this.updateVisibility}>
                     {this.categories.map(category => (
                         <Category key={category.id} id={category.id} name={category.name}
                             emojis={this.memoizedDataByCategory[category.id]} onClick={this.onClickEmoji}
diff --git a/src/components/views/emojipicker/Header.js b/src/components/views/emojipicker/Header.js
index 95af68f4a6..04addfc81d 100644
--- a/src/components/views/emojipicker/Header.js
+++ b/src/components/views/emojipicker/Header.js
@@ -19,33 +19,20 @@ import PropTypes from 'prop-types';
 
 import * as icons from "./icons";
 
-class Header extends React.Component {
+class Header extends React.PureComponent {
     static propTypes = {
         categories: PropTypes.arrayOf(PropTypes.object).isRequired,
         onAnchorClick: PropTypes.func.isRequired,
-        defaultCategory: PropTypes.string,
-    };
-
-    constructor(props) {
-        super(props);
-        this.state = {
-            selected: props.defaultCategory || props.categories[0].id,
-        };
-        this.handleClick = this.handleClick.bind(this);
-    }
-
-    handleClick(selected) {
-        this.setState({selected});
-        this.props.onAnchorClick(selected);
+        refs: PropTypes.object,
     };
 
     render() {
         return (
             <nav className="mx_EmojiPicker_header">
                 {this.props.categories.map(category => (
-                    <button disabled={!category.enabled} key={category.id} className={`mx_EmojiPicker_anchor ${
-                        this.state.selected === category.id ? 'mx_EmojiPicker_anchor_selected' : ''}`}
-                        onClick={() => this.handleClick(category.id)} title={category.name}>
+                    <button disabled={!category.enabled} key={category.id} ref={category.ref}
+                        className={`mx_EmojiPicker_anchor ${category.visible ? 'mx_EmojiPicker_anchor_visible' : ''}`}
+                        onClick={() => this.props.onAnchorClick(category.id)} title={category.name}>
                         {icons.categories[category.id]()}
                     </button>
                 ))}